| BEDTools vcf flanking sequence | mmassaviol | MBBstable
| vcf postprocess | BEDTools to obtain the flanking sequence of each variant in the VCF. | 2.31 | websitegitdoc | doi: 10.1093/bioinformatics/btq033 | |
| CIAlign | mmassaviol | MBBstable
| phylogenetics | command line tool which performs various functions to clean and analyse a multiple sequence alignment (MSA) | 1.0.18 | websitegitdoc | 10.7717/peerj.12983 | |
| FROGS affiliation | mmassaviol | MBBstable
| FROGS | Adding taxonomic affiliation in abundance file | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS affiliation customDB | mmassaviol | MBBstable
| FROGS | Adding taxonomic affiliation in abundance file | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS biom2tsv | mmassaviol | MBBstable
| FROGS | Adding taxonomic affiliation in abundance file | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS cluster | mmassaviol | MBBstable
| FROGS | Single-linkage clustering on sequences | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS filter OTU | mmassaviol | MBBstable
| FROGS | Filters OTUs on several criteria | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS filter affiliation | mmassaviol | MBBstable
| FROGS | Filters OTUs on several affiliation criteria | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS phyloseq_stats | mmassaviol | MBBstable
| FROGS | Phyloseq to analyse abundance, diversity and structure | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS preprocess | mmassaviol | MBBstable
| FROGS | Merging, Denoising and Dereplication | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FROGS remove chimera | mmassaviol | MBBstable
| FROGS | Remove PCR chimera in each sample | 4.1.0 | websitegitdoc | 10.1093/bib/bbab318 | |
| FstPiDxy_Manhattan | mmassaviol | MBBstable
| genet pop | Manhattan plot of Fs, Pi and Dxy pairwise values on sliding windows | 1.38.0 | websitegit | | |
| W&C Fst | mmassaviol | MBBstable
| genet pop | W&C Fixation index (Fst) with SNPRelate R package | 1.32.0 | | | |
| identity-by-state IBS | mmassaviol | MBBstable
| genet pop | identity-by-state (IBS) estimation with SNPRelate of the fraction of identity by state for each pair of samples | 1.32.0 | | | |
| KMC | mmassaviol | MBBstable
| quantification | KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files | 3.2.1 | websitegitdoc | | |
| Picard Mark Duplicates | mmassaviol | MBBstable
| bam correction | This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. | 3.0.0 | websitegitdoc | | |
| identity-by-descent IBD | mmassaviol | MBBstable
| genet pop | identity-by-descent (IBD) estimation in SNPRelate either with the method of moments (MoM) (Purcell et al., 2007) or maximum likelihood estimation (MLE) (Milligan, 2003; Choi et al., 2009) | | | | |
| VSEARCH generate abundance table | mmassaviol | MBBstable
| VSEARCH | Search strictly identical sequences contained for each sample fasta file presents in a fasta file (OTU/ZOTU/ASV database) | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH Unoise rm chimera OTU | mmassaviol | MBBstable
| VSEARCH | Denoising of the fasta sequences in filename according to the UNOISE3 algorithm (Robert Edgar), chimera removal and OTU output | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH clustering rm chimera generate OTU Table | mmassaviol | MBBstable
| VSEARCH | Clustering of the fasta sequences in filename according to the UCLUST algorithm (Robert Edgar), chimera removal and OTU output | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH Dereplicate | mmassaviol | MBBstable
| VSEARCH | Merge strictly identical sequences contained in fasta files in a dir and relabel | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH Dereplicate file | mmassaviol | MBBstable
| VSEARCH | Merge strictly identical sequences contained in fasta file | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH Filter | mmassaviol | MBBstable
| VSEARCH | Filter fastqc reads and produce fasta files | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH MergePairs | mmassaviol | MBBstable
| VSEARCH | Merge paired-end reads into one sequence | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH stats | mmassaviol | MBBstable
| VSEARCH | quality score and expected error statistics | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| VSEARCH Unoise rm chimera generate ZOTU Table | mmassaviol | MBBstable
| VSEARCH | Denoising of the fasta sequences in filename according to the UNOISE3 algorithm (Robert Edgar), chimera removal and ZOTU output | 2.23.0 | gitdoc | 10.7717/peerj.2584 | |
| ABRicate | mmassaviol | MBBstable
| metagenomic | Mass screening of contigs for antimicrobial resistance or virulence genes | 1.0.1 | websitegitdoc | | |
| ABySS | mmassaviol | MBBstable
| assembly | ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes. | 2.3.7 | websitegitdoc | 10.1101/gr.214346.116 | |
| Accel-align is a fast alignment tool implemented in C++ | mmassaviol | MBBstable
| mapping | a fast sequence mapper and aligner based on the seed-embed-extend method | 2.0 | websitegitdoc | 10.1186/s12859-021-04162-z | |
| Accel-align is a fast alignment tool implemented in C++ | mmassaviol | MBBstable
| indexing | a fast sequence mapper and aligner based on the seed-embed-extend method | 2.0 | websitegitdoc | 10.1186/s12859-021-04162-z | |
| expand bams to a bams_Dir | mmassaviol | MBBstable
| format conversion | Create a Dir with symlinks to bams in input | | | | |
| Bcftools Merge VCFs | mmassaviol | MBBstable
| format conversion | Merge multiple VCF or BCF files to create one multi-sample file combining compatible records into one | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| BCFtools mpileup and call | mmassaviol | MBBstable
| variant calling | BCFtools mpileup on each sample. | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| BCFtools mpileup and call jointly all bams in a dir | mmassaviol | MBBstable
| variant calling | BCFtools mpileup is called jointly on all bams in a dir . | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| BCFtools VCF Stats | mmassaviol | MBBstable
| vcf postprocess | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| BCFtools VCF Stats | mmassaviol | MBBstable
| vcf postprocess | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| BEAST | mmassaviol | MBBstable
| phylogenetics | BEAST 2: cross-platform program for Bayesian phylogenetic analysis of molecular sequences | 2.6.3 | websitegitdoc | DOI:10.1371/journal.pcbi.1006650 | |
| blast snp2outgroup | mmassaviol | MBBstable
| blast | BLAST programs search nucleotide databases using a nucleotide query | 2.14.0 | websitedoc | 10.1186/1471-2105-10-421 | |
| BlastN | mmassaviol | MBBstable
| blast | BLASTN programs search nucleotide databases using a nucleotide query | 2.14.0 | websitedoc | 10.1186/1471-2105-10-421 | |
| BlastN NCBI | mmassaviol | MBBstable
| blast | BLASTN programs search nucleotide databases using a nucleotide query | 2.14.0 | websitedoc | 10.1186/1471-2105-10-421 | |
| Bowtie | mmassaviol | MBBstable
| mapping | Bowtie is an ultrafast, memory-efficient short read aligner. | 1.3.1 | websitegitdoc | 10.1002/0471250953.bi1107s32 | |
| Bowtie2 | mmassaviol | MBBstable
| mapping | A fast and sensitive gapped read aligner | 2.5.1 | websitegitdoc | 10.1038/nmeth.1923 | |
| Bowtie2 index | mmassaviol | MBBstable
| indexing | A fast and sensitive gapped read aligner | 2.5.1 | websitegitdoc | 10.1038/nmeth.1923 | |
| Bowtie index | mmassaviol | MBBstable
| indexing | Bowtie is an ultrafast, memory-efficient short read aligner. | 1.3.1 | websitegitdoc | 10.1002/0471250953.bi1107s32 | |
| Busco | mmassaviol | MBBstable
| post assembly | Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50. | 5.4.7 | websitegitdoc | 10.1007/978-1-4939-9173-0_14 | |
| BWA MEM (Burrows-Wheeler Alignment Tool) | mmassaviol | MBBstable
| mapping | BWA is a software package for mapping low-divergent sequences against a large reference genome. | 0.7.17 | websitegitdoc | 10.1093/bioinformatics/btp324 | |
| BWA MEM2 (Burrows-Wheeler Alignment Tool) | mmassaviol | MBBstable
| mapping | Bwa mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster (WIP; not recommended for production uses at the moment) | 2.2.1 | websitegitdoc | 10.1109/IPDPS.2019.00041 | |
| BWA MEM2 index | mmassaviol | MBBstable
| indexing | Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster (WIP; not recommended for production uses at the moment) | 2.2.1 | websitegitdoc | 10.1109/IPDPS.2019.00041 | |
| BWA MEM index | mmassaviol | MBBstable
| indexing | BWA is a software package for mapping low-divergent sequences against a large reference genome. | 0.7.17 | websitegitdoc | 10.1093/bioinformatics/btp324 | |
| Compare VCFs | mmassaviol | MBBstable
| vcf postprocess | Compare several VCF files | 1.2.0 | websitegitdoc | 10.21105/joss.01144 | |
| Compare VCFs inDir(bcftools) | mmassaviol | MBBstable
| vcf postprocess | Compare several VCF files | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| Compare VCFs (bcftools) | mmassaviol | MBBstable
| vcf postprocess | Compare several VCF files DONT USE FOR NOW | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| cstacks | mmassaviol | MBBstable
| stacks | cstacks creates a set of consensus loci, merging alleles together. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| Cutadapt | mmassaviol | MBBstable
| quality | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | 4.4 | websitegitdoc | 10.14806/ej.17.1.200 | |
| dada2 | mmassaviol | MBBstable
| metabarcoding | Fast and accurate sample inference from amplicon data with single-nucleotide resolution | 1.26 | websitegitdoc | 10.1038/nmeth.3869 | |
| dada2_Err_Derep_makeSequenceTable | mmassaviol | MBBstable
| metabarcoding | Learn the Error Rates, dereplicate, Merge paired reads, Construct sequence table and Remove chimeras | 1.26 | websitegitdoc | 10.1038/nmeth.3869 | |
| dada2_assign_taxonomy | mmassaviol | MBBstable
| metabarcoding | Fast and accurate sample inference from amplicon data with single-nucleotide resolution | 1.26 | websitegitdoc | 10.1038/nmeth.3869 | |
| dada2_assign_taxonomy_customDB | mmassaviol | MBBstable
| metabarcoding | Fast and accurate sample inference from amplicon data with single-nucleotide resolution | 1.26 | websitegitdoc | 10.1038/nmeth.3869 | |
| dada2_filter_trim | mmassaviol | MBBstable
| metabarcoding | Fast and accurate sample inference from amplicon data with single-nucleotide resolution | 1.26 | websitegitdoc | 10.1038/nmeth.3869 | |
| dada2_plotQualityProfile | mmassaviol | MBBstable
| metabarcoding | Fast and accurate sample inference from amplicon data with single-nucleotide resolution | 1.26 | websitegitdoc | 10.1038/nmeth.3869 | |
| dadi | mmassaviol | MBBstable
| genet pop | Fit population genetic models of demography and selection using diffusion approximations to the allele frequency spectrum | 2.3.0 | websitegitdoc | 10.1038/npre.2010.4594.1 | |
| DeepVariant | mmassaviol | MBBstable
| variant calling | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. | 0.9.0 | websitegitdoc | 10.1038/nbt.4235 | |
| demultiplexing_astrid_cruaud | mmassaviol | MBBstable
| other | | | | 10.1111/1755-0998.13006 | |
| DESeq2 | mmassaviol | MBBstable
| differential expression | Differential gene expression analysis based on the negative binomial distribution. Using normalized count data. | 1.38 | websitegitdoc | 10.1186/s13059-014-0550-8 | |
| edgeR | mmassaviol | MBBstable
| differential expression | Empirical Analysis of Digital Gene Expression Data. | 3.40.0 | websitegitdoc | 10.18129/B9.bioc.edgeR | |
| est sfs | mmassaviol | MBBstable
| other | BLAST programs search nucleotide databases using a nucleotide query | 2.04 | websitedoc | https://doi.org/10.1534/genetics.118.301120 | |
| fastStructure | mmassaviol | MBBstable
| genet pop | A fast algorithm for inferring population structure from large SNP genotype data | 1.0 | websitegit | Anil Raj, Matthew Stephens, and Jonathan K. Pritchard. fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets, (Genetics) June 2014 197:573-589 | |
| fastStructure_gds | mmassaviol | MBBstable
| genet pop | A fast algorithm for inferring population structure from large SNP genotype data | | websitegit | Anil Raj, Matthew Stephens, and Jonathan K. Pritchard. fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets, (Genetics) June 2014 197:573-589 | |
| fasta to phylip | mmassaviol | MBBstable
| format conversion | Conversion of an aligned fasta file to phylip format | | | | |
| fasta merge | mmassaviol | MBBstable
| format conversion | Concatenate all fasta files in a dir into a single fasta file | | | | |
| fastp | mmassaviol | MBBstable
| quality | A tool designed to provide fast all-in-one preprocessing for FastQ files. | 0.23.4 | websitegitdoc | 10.1093/bioinformatics/bty560 | |
| fastq to fasta | mmassaviol | MBBstable
| format conversion | Conversion of a fastq file to a fasta file | | | | |
| FastQC | mmassaviol | MBBstable
| quality | A quality control tool for high throughput raw sequence data. | 0.12.1 | websitegitdoc | | |
| FLASH | mmassaviol | MBBstable
| sequence manipulation | FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments | 1.2.11 | websitegitdoc | 10.1093/bioinformatics/btr507 | |
| flye | mmassaviol | MBBstable
| assembly | Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. | 2.9.2 | websitegitdoc | s41592-020-00971-x | |
| freebayes | mmassaviol | MBBstable
| variant calling | Bayesian haplotype-based genetic polymorphism discovery and genotyping | 1.3.6 | websitegitdoc | arxiv.org/abs/1207.3907 | |
| GATK3 Indel Realigner | mmassaviol | MBBstable
| bam correction | The local realignment process is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases is minimized across all the reads. | 3.8 | websitedoc | | |
| GATK3 Haplotype Caller | mmassaviol | MBBstable
| variant calling | The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region | 3.8 | websitedoc | 10.1101/gr.107524.110 | |
| GATK3 prepare fasta | mmassaviol | MBBstable
| indexing | Prepare fasta ref for GATK | 3.0 | | | |
| Gblocks | mmassaviol | MBBstable
| phylogenetics | Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. | 0.91b | websitedoc | 10.1093/oxfordjournals.molbev.a026334 | |
| GenomeScope | mmassaviol | MBBstable
| quality | Fast genome analysis from unassembled short reads | 2.0.0 | websitegitdoc | 10.1038/s41467-020-14998-3 | |
| GetOrganelle | mmassaviol | MBBstable
| find mito scaffold | This toolkit assembles organelle genome from genomic skimming data. | 1.7.7.0 | websitegitdoc | 10.1186/s13059-020-02154-5 | |
| ggtree draw tree | mmassaviol | MBBstable
| phylogenetics | R package for visualization of phylogenetic trees with their annotation data | 3.6.0 | websitegitdoc | abs/10.1002/cpbi.96 | |
| gstacks_denovo | mmassaviol | MBBstable
| stacks | gstacks build loci from the single and/or paired-end reads before calling SNPs | 2.64 | websitedoc | 10.1111/mec.15253 | |
| gstacks_refMap | mmassaviol | MBBstable
| stacks | gstacks build loci from the single and/or paired-end reads before calling SNPs | 2.64 | websitedoc | 10.1111/mec.15253 | |
| guppy | mmassaviol | MBBstable
| basecalling | Basecalling, the process of converting raw signal data into a sequence | latest | websitegitdoc | https://nanoporetech.com/ | |
| Hisat2 | mmassaviol | MBBstable
| mapping | a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) | 2.2.1 | websitegitdoc | Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019). | |
| hisat2 index | mmassaviol | MBBstable
| indexing | a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) | 2.2.1 | websitegitdoc | Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019). | |
| Htseq count | mmassaviol | MBBstable
| quantification | A tool to quantify gene expression in RNA-Seq and similar experiments. | 2.0.3 | websitegitdoc | doi:10.1093/bioinformatics/btu638 | |
| IGV visualize | mmassaviol | MBBstable
| visualization | Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations | 2.13.2 | websitegitdoc | 10.1038/nbt.1754 | |
| interop | mmassaviol | MBBstable
| visualization | The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files. | 1.2.4 | websitegitdoc | | |
| IQ-TREE | mmassaviol | MBBstable
| phylogenetics | Efficient software for phylogenomic inference | 2.2.2.7 | websitegitdoc | 10.1093/molbev/msu300 | |
| JELLYFISH count | mmassaviol | MBBstable
| quantification | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence | 2.3.0 | websitegitdoc | 10.1093/bioinformatics/btr011 | |
| JELLYFISH histo | mmassaviol | MBBstable
| visualization | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence | 2.3.0 | websitegitdoc | 10.1093/bioinformatics/btr011 | |
| jmodeltest2 | mmassaviol | MBBstable
| phylogenetics | jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution | 2.1.10 | websitegitdoc | 10.1080/10635150390235520 | |
| kallisto index | mmassaviol | MBBstable
| indexing | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | 0.48.0 | websitegitdoc | 10.1038/nbt.3519 | |
| kallisto quant | mmassaviol | MBBstable
| quantification | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | 0.48.0 | websitegitdoc | 10.1038/nbt.3519 | |
| lastz | mmassaviol | MBBstable
| blast | A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically | 1.04.15 | websitegitdoc | | |
| lulu post clustering | mmassaviol | MBBstable
| metabarcoding | A r-package for distribution based post clustering curation of amplicon data. | 1.0.0 | websitegitdoc | https://www.nature.com/articles/s41467-017-01312-x | |
| MAFFT | mmassaviol | MBBstable
| phylogenetics | MAFFT: a multiple sequence alignment program | 7.520 | websitegitdoc | 10.1093/molbev/mst010 | |
| Make Blast database | mmassaviol | MBBstable
| blast | Make Blast database | 2.14.0 | websitedoc | 10.1186/1471-2105-10-421 | |
| Mapping box | mmassaviol | MBBstable
| mapping | Takes reads and fasta reference and returns a bam and stats | | | | |
| medaka | mmassaviol | MBBstable
| post assembly | Medaka is a tool to create a consensus sequence of nanopore sequencing data. | 1.8.0 | websitegitdoc | | |
| MEGAHIT | mmassaviol | MBBstable
| assembly | An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | 1.2.9 | websitegitdoc | 10.1016/j.ymeth.2016.02.020 | |
| MetaBAT1 | mmassaviol | MBBstable
| metagenomic | Metagenome Binning based on Abundance and Tetranucleotide frequency | 1.2.15 | websitegitdoc | 10.7717/peerj.1165 | |
| miniasm | mmassaviol | MBBstable
| assembly | Ultrafast de novo assembly for long noisy reads (though having no consensus step) | 0.3 | websitegitdoc | 10.1093/bioinformatics/btw152 | |
| minimap2 overlap | mmassaviol | MBBstable
| mapping | A versatile pairwise aligner for genomic and spliced nucleotide sequences | 2.26 | websitegitdoc | 10.1093/bioinformatics/bty191 | |
| minimap2 overlap self | mmassaviol | MBBstable
| mapping | A versatile pairwise aligner for genomic and spliced nucleotide sequences | 2.26 | websitegitdoc | 10.1093/bioinformatics/bty191 | |
| minimap2 reference | mmassaviol | MBBstable
| mapping | A versatile pairwise aligner for genomic and spliced nucleotide sequences | 2.26 | websitegitdoc | 10.1093/bioinformatics/bty191 | |
| minimap2 reference_bam | mmassaviol | MBBstable
| mapping | A versatile pairwise aligner for genomic and spliced nucleotide sequences | 2.26 | websitegitdoc | 10.1093/bioinformatics/bty191 | |
| MitoZ annotate | mmassaviol | MBBstable
| annotation | A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes | 3.5 | websitegitdoc | 10.1093/nar/gkz173 | |
| MitoZ assemble and find mitogenome | mmassaviol | MBBstable
| assembly | A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes | 3.5 | websitegitdoc | 10.1093/nar/gkz173 | |
| MitoZ filter | mmassaviol | MBBstable
| quality | A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes: Filter using fastp | 3.5 | websitegitdoc | 10.1093/nar/gkz173 | |
| MitoZ find mito scaffold | mmassaviol | MBBstable
| find mito scaffold | A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes | 3.5 | websitegitdoc | 10.1093/nar/gkz173 | |
| moments infer 2D model | mmassaviol | MBBstable
| genet pop | moments implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. | 1.1.16 | websitegitdoc | 10.1534/genetics.117.200493 | |
| plot 2D sfs | mmassaviol | MBBstable
| genet pop | moments implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. | 1.1.16 | websitegitdoc | 10.1534/genetics.117.200493 | |
| multiSamplesvcfparser | mmassaviol | MBBstable
| vcf postprocess | Plot stats for a multisample VCF file | | websitegitdoc | | |
| MUSCLE | mmassaviol | MBBstable
| phylogenetics | Multiple sequence alignment | 5.1 | websitegitdoc | 10.1093/nar/gkh340 | |
| nanoplot_fastq | mmassaviol | MBBstable
| quality | nanoplot is a plotting tool for long read sequencing data and alignments | 1.41.6 | websitegitdoc | 10.1093/bioinformatics/bty149 | |
| nanoplot_summary_file | mmassaviol | MBBstable
| quality | nanoplot is a plotting tool for long read sequencing data and alignments | 1.41.6 | websitegitdoc | 10.1093/bioinformatics/bty149 | |
| octopus | mmassaviol | MBBstable
| variant calling | Bayesian haplotype-based mutation calling | 0.7.4 | websitegitdoc | https://doi.org/10.1038/s41587-021-00861-3 | |
| Principal Component Analysis | mmassaviol | MBBstable
| genet pop | Principal Component Analysis (PCA) on genotypes with SNPRelate R package | 0.3.3 | | | |
| phylip to fasta | mmassaviol | MBBstable
| format conversion | Conversion of a phylip file to an aligned fasta | 1.81 | | | |
| Stacks populations | mmassaviol | MBBstable
| stacks | The populations program will analyze a population of individual samples computing a number of population genetics statistics as well as exporting a variety of standard output formats. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| process_radtags | mmassaviol | MBBstable
| stacks | process_radtags examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| process_shortreadstags | mmassaviol | MBBstable
| stacks | Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| QUAST | mmassaviol | MBBstable
| quality | Quality Assessment Tool for Genome Assemblies | 5.2.0 | websitegitdoc | 10.1093/bioinformatics/btt086 | |
| Racon | mmassaviol | MBBstable
| post assembly | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads | 1.5.0 | websitegitdoc | 10.1101/gr.214270.116 | |
| radsex_distrib | mmassaviol | MBBstable
| radsex | Computing the distribution of all markers between males and females | latest | websitegitdoc | https://doi.org/10.1111/1755-0998.13360 | |
| radsex_map | mmassaviol | MBBstable
| radsex | Aligning markers to a genome and computing bias and probability of association with group for each aligned marker | latest | websitegitdoc | https://doi.org/10.1111/1755-0998.13360 | |
| radsex_process | mmassaviol | MBBstable
| radsex | Creating a table of marker depths from processed radtag reads | latest | websitegitdoc | https://doi.org/10.1111/1755-0998.13360 | |
| radsex_processTagged | mmassaviol | MBBstable
| radsex | Creating a table of marker depths from radtag reads containing index tags | latest | websitegitdoc | https://doi.org/10.1111/1755-0998.13360 | |
| radsex_signif | mmassaviol | MBBstable
| radsex | Extracting all markers significantly associated with sex | latest | websitegitdoc | https://doi.org/10.1111/1755-0998.13360 | |
| RAxML-NG | mmassaviol | MBBstable
| phylogenetics | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion | 1.2.0 | websitegitdoc | 10.1093/bioinformatics/btz305 | |
| Salmon index | mmassaviol | MBBstable
| indexing | Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. | 1.10.2 | websitegitdoc | 10.1038/nmeth.4197 | |
| Salmon quant | mmassaviol | MBBstable
| quantification | Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. | 1.10.2 | websitegitdoc | 10.1038/nmeth.4197 | |
| SAM to phylip | mmassaviol | MBBstable
| quality | Conversion of SAM files to phylip format by grouping sample entries by reference sequence | 6.6.0 | | | |
| Add Read Group to Bam | mmassaviol | MBBstable
| bam correction | The program adds or replace read group tags in a file | 1.17 | websitegitdoc | 10.1093/bioinformatics/btp352 | |
| SAM tools stats | mmassaviol | MBBstable
| quality | The program collects statistics from BAM files | 1.17 | websitegitdoc | 10.1093/bioinformatics/btp352 | |
| sfs outgroup | mmassaviol | MBBstable
| blast | BLAST programs search nucleotide databases using a nucleotide query | 2.14.0 | websitegitdoc | 10.1186/1471-2105-10-421 | |
| Coalescent Simulation | mmassaviol | MBBstable
| genet pop | | | | | |
| smudgeplotJelly | mmassaviol | MBBstable
| quantification | Tool intended for genome profiling (assembly-less understanding of genomes from sequencing reads) in combo with Genomescope | 0.2.5 | websitegitdoc | https://doi.org/10.1038/s41467-020-14998-3 | |
| smudgeplotKMC | mmassaviol | MBBstable
| quantification | Tool intended for genome profiling (assembly-less understanding of genomes from sequencing reads) in combo with Genomescope | 0.2.5 | websitegitdoc | https://doi.org/10.1038/s41467-020-14998-3 | |
| Scalable Nucleotide Alignment Program | mmassaviol | MBBstable
| mapping | fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and align them quickly through a hash-based indexing scheme. | 2.0.3 | websitegitdoc | arXiv:1111.5572v1 | |
| Scalable Nucleotide Alignment Program | mmassaviol | MBBstable
| indexing | fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and align them quickly through a hash-based indexing scheme. | 2.0.3 | websitegitdoc | arXiv:1111.5572v1 | |
| snom | mmassaviol | MBBstable
| other | Find out homologous of specific base of a query sequence in blast results | 0.1.0 | git | | |
| SPAdes | mmassaviol | MBBstable
| assembly | SPAdes is an assembly toolkit containing various assembly pipelines. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. | 3.15.5 | websitegitdoc | 10.1089/cmb.2012.0021 | |
| sstacks | mmassaviol | MBBstable
| stacks | Sets of stacks, i.e. putative loci, constructed by the ustacks program can be searched against a catalog produced by cstacks. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles. In the case of a general population, all samples in the population would be matched against the catalog with sstacks. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| T-lex3 | mmassaviol | MBBstable
| blast | T-lex is a computational pipeline that detects presence and/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data. | 3.0 | websitegitdoc | 10.1093/bioinformatics/btz727 | |
| TransDecoder | mmassaviol | MBBstable
| post assembly | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | 5.7.1 | websitegitdoc | | |
| Transrate | mmassaviol | MBBstable
| quality | Transrate is software for de-novo transcriptome assembly quality analysis. | 1.0.3 | websitegitdoc | 10.1101/gr.196469.115 | |
| trimAl | mmassaviol | MBBstable
| phylogenetics | trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment | 1.4.1 | websitegitdoc | 10.1093/bioinformatics/btp348 | |
| Trimmomatic | mmassaviol | MBBstable
| quality | A flexible read trimming tool for Illumina NGS data | 0.39 | websitedoc | 10.1093/bioinformatics/btu170 | |
| Trinity | mmassaviol | MBBstable
| assembly | Trinity assembles transcript sequences from Illumina RNA-Seq data. | 2.15.1 | websitegitdoc | 10.1038/nbt.1883 | |
| tsv2bam | mmassaviol | MBBstable
| stacks | This program will transpose data so that it is oriented by locus, instead of by sample. In additon, if paired-ends are available, the program will pull in the set of paired reads that are associate with each single-end locus that was assembled de novo. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| ustacks | mmassaviol | MBBstable
| stacks | The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks (or putative alleles). Comparing the stacks it will form a set of putative loci and detect SNPs at each locus using a maximum likelihood framework. | 2.64 | websitedoc | 10.1111/mec.15253 | |
| vcf to gds | mmassaviol | MBBstable
| format conversion | Conversion of an vcf file to gds format with seqArray R package | | | | |
| vcf annotate | mmassaviol | MBBstable
| vcf postprocess | BCFtools annotate to append a new INFO in a vcf. | 1.17 | websitegitdoc | 10.1093/bioinformatics/btr509 | |
| Plot VCF (deepvariant) | mmassaviol | MBBstable
| vcf postprocess | Plot VCF stats with deepvariant | 0.9.0 | websitegitdoc | 10.1038/nbt.4235 | |
| VCFparser | mmassaviol | MBBstable
| vcf postprocess | Plot VCF stats | | websitegitdoc | | |
| vcftools allelic variants count sfs | mmassaviol | MBBstable
| vcf postprocess | VCFtools to count the allele frequency of each variant and convert to partial est-sfs format input. | 0.1.16 | websitegitdoc | http://dx.doi.org/10.1093/bioinformatics/btr330 | |
| Velvet | mmassaviol | MBBstable
| assembly | Velvet is a de novo genomic assembler specially designed for short read sequencing technologies. | 1.2.10 | websitegitdoc | 10.1101/gr.074492.107 | |