[ { "id": "dada2", "name": "dada2", "article": "10.1038\/nmeth.3869", "website": "https:\/\/benjjneb.github.io\/dada2", "git": "https:\/\/github.com\/benjjneb\/dada2", "description": "Fast and accurate sample inference from amplicon data with single-nucleotide resolution", "version": "1.26", "documentation": "https:\/\/benjjneb.github.io\/dada2", "multiqc": "custom", "commands": [ { "name": "dada2", "command": null, "category": "metabarcoding", "output_dir": "dada2", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" } ], "outputs": [ { "name": "qualityForward", "type": "png", "file": "Quality_forward_mqc.png", "description": "Quality graph of the forward reads of the first two samples" }, { "name": "qualityReverse", "type": "png", "file": "Quality_reverse_mqc.png", "description": "Quality graph of the reverse reads of the first two samples" }, { "name": "filter_and_trim_out", "type": "rds", "file": "filter_and_trim_out.rds", "description": "Post-filter and trimming report" }, { "name": "filtFs", "type": "fastq.gz", "file": "filtered\/{sample}_F_filt.fastq.gz", "description": "List of filtered forward reads" }, { "name": "filtRs", "type": "fastq.gz", "file": "filtered\/{sample}_R_filt.fastq.gz", "description": "List of filtered reverse reads" }, { "name": "errorsForward", "type": "png", "file": "Errors_forward_mqc.png", "description": "Error rate graph on forward reads" }, { "name": "errorsReverse", "type": "png", "file": "Errors_reverse_mqc.png", "description": "Error rate graph on reverse reads" }, { "name": "errF_rds", "type": "rds", "file": "errF.rds", "description": "Error prediction for forward reads" }, { "name": "errR_rds", "type": "rds", "file": "errR.rds", "description": "Error prediction for reverse reads" }, { "name": "track", "type": "tsv", "file": "Track_reads_mqc.tsv", "description": "Read count in the different steps" }, { "name": "seqtab", "type": "rds", "file": "seqtab.rds", "description": "Sequence table" }, { "name": "seqtab_nochim_csv", "type": "csv", "file": "seqtab_nochim.csv", "description": "Sequence table after removal of chimeras" }, { "name": "seqtab_nochim_rds", "type": "rds", "file": "seqtab_nochim.rds", "description": "Sequence table after removal of chimeras" }, { "name": "uniques_nochim", "type": "contigs", "file": "uniques_nochim.fasta", "description": "Unique sequences after removal of chimeras" }, { "name": "taxa_bootstrap", "type": "tsv", "file": "Taxa_bootstrap_mqc.tsv", "description": "Bootstrap of taxa" }, { "name": "taxa_rds", "type": "rds", "file": "taxa.rds", "description": "Taxa" }, { "name": "otu_table", "type": "csv", "file": "otu_table.csv", "description": "OTU table" }, { "name": "tax_table_csv", "type": "csv", "file": "tax_table.csv", "description": "Taxa table" }, { "name": "richness", "type": "png", "file": "Richness_mqc.png", "description": "Richness plot" }, { "name": "top20", "type": "png", "file": "Top_20_mqc.png", "description": "Top 20 OTU" }, { "name": "ps_out", "type": "rds", "file": "ps_out.rds", "description": "Phyloseq object" }, { "name": "ordination", "type": "png", "file": "Ordination_mqc.png", "description": "Ordination plot" }, { "name": "tax_table_biom", "type": "txt", "file": "tax_table.qiime.txt", "description": "Taxa table for qiime" }, { "name": "out_table_biom", "type": "biom", "file": "otu_table.qiime.biom", "description": "OTU table for qiime" } ], "options": [ { "name": "dada2_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "dada2_no_filter_and_trim", "prefix": null, "type": "checkbox", "value": false, "label": "Skip filter and trim step" }, { "name": "dada2_remove_chim", "prefix": null, "type": "checkbox", "value": true, "label": "Remove chimeras" }, { "name": "dada2_taxonomypath", "type": "select", "choices": [ { "silva138 (16S)": "\/taxonomy\/silva138" }, { "silva132 (16S)": "\/taxonomy\/silva132" }, { "silva128 (16S)": "\/taxonomy\/silva128" }, { "rdp16 (16S)": "\/taxonomy\/rdp16" }, { "greengenes13.8 (16S)": "\/taxonomy\/gg13_8" }, { "unite_8.2 (ITS)": "\/taxonomy\/unite_8.2" }, { "unite_2_2_2019 (ITS)": "\/taxonomy\/unite_2_2_2019" }, { "midori_COI (COI)": "\/taxonomy\/midori_coi" }, { "midori_COI_Without_Terrestrial (COI)": "\/taxonomy\/midori_coi_wo_terrestrial" }, { "refseq-rdp16s (16S)": "\/taxonomy\/refseq-rdp16s" } ], "value": "silva138 (16S)", "label": "Taxonomy source" }, { "name": "dada2_truncLen_forward", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": 1, "label": "truncLen forward : Truncate reads after truncLen bases. Reads shorter than this are discarded" }, { "name": "dada2_truncLen_reverse", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": 1, "label": "truncLen reverse : Truncate reads after truncLen bases. Reads shorter than this are discarded" }, { "name": "dada2_maxEE_forward", "type": "numeric", "value": -1, "min": -1, "max": "NA", "step": 1, "label": "maxEE forward : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering)." }, { "name": "dada2_maxEE_reverse", "type": "numeric", "value": -1, "min": -1, "max": "NA", "step": 1, "label": "maxEE reverse : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering)." } ] } ], "install": [], "script": "dada2.script.R", "data": [ { "name": "taxonomy", "type": "directory" } ], "citations": { "dada2": [ "Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038\/nmeth.3869" ], "phyloseq": [ "McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217" ], "biomformat": [ "Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, Volume 1, Issue 1, December 2012, 2047-217X-1-7, https:\/\/doi.org\/10.1186\/2047-217X-1-7" ], "krona": [ "Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385" ] }, "yaml": "{\n id: dada2,\n name: dada2,\n article: 10.1038\/nmeth.3869,\n website: \"https:\/\/benjjneb.github.io\/dada2\",\n git: \"https:\/\/github.com\/benjjneb\/dada2\",\n description: \"Fast and accurate sample inference from amplicon data with single-nucleotide resolution\",\n version: \"1.26\",\n documentation: \"https:\/\/benjjneb.github.io\/dada2\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: dada2,\n command: ~,\n category: \"metabarcoding\",\n output_dir: dada2,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n outputs: [\n { name: qualityForward, type: \"png\", file: \"Quality_forward_mqc.png\", description: \"Quality graph of the forward reads of the first two samples\" },\n { name: qualityReverse, type: \"png\", file: \"Quality_reverse_mqc.png\", description: \"Quality graph of the reverse reads of the first two samples\" },\n { name: filter_and_trim_out, type: \"rds\", file: \"filter_and_trim_out.rds\", description: \"Post-filter and trimming report\" },\n { name: filtFs, type: \"fastq.gz\", file: \"filtered\/{sample}_F_filt.fastq.gz\", description: \"List of filtered forward reads\" },\n { name: filtRs, type: \"fastq.gz\", file: \"filtered\/{sample}_R_filt.fastq.gz\", description: \"List of filtered reverse reads\" },\n { name: errorsForward, type: \"png\", file: \"Errors_forward_mqc.png\", description: \"Error rate graph on forward reads\" },\n { name: errorsReverse, type: \"png\", file: \"Errors_reverse_mqc.png\", description: \"Error rate graph on reverse reads\" },\n { name: errF_rds, type: \"rds\", file: \"errF.rds\", description: \"Error prediction for forward reads\" },\n { name: errR_rds, type: \"rds\", file: \"errR.rds\", description: \"Error prediction for reverse reads\" },\n { name: track, type: \"tsv\", file: \"Track_reads_mqc.tsv\", description: \"Read count in the different steps\" },\n { name: seqtab, type: \"rds\", file: \"seqtab.rds\", description: \"Sequence table\" },\n { name: seqtab_nochim_csv, type: \"csv\", file: \"seqtab_nochim.csv\", description: \"Sequence table after removal of chimeras\" },\n { name: seqtab_nochim_rds, type: \"rds\", file: \"seqtab_nochim.rds\", description: \"Sequence table after removal of chimeras\" },\n { name: uniques_nochim, type: \"contigs\", file: \"uniques_nochim.fasta\", description: \"Unique sequences after removal of chimeras\" },\n { name: taxa_bootstrap, type: \"tsv\", file: \"Taxa_bootstrap_mqc.tsv\", description: \"Bootstrap of taxa\" },\n { name: taxa_rds, type: \"rds\", file: \"taxa.rds\", description: \"Taxa\" },\n { name: otu_table, type: \"csv\", file: \"otu_table.csv\", description: \"OTU table\" },\n { name: tax_table_csv, type: \"csv\", file: \"tax_table.csv\", description: \"Taxa table\" },\n { name: richness, type: \"png\", file: \"Richness_mqc.png\", description: \"Richness plot\" },\n { name: top20, type: \"png\", file: \"Top_20_mqc.png\", description: \"Top 20 OTU\" },\n { name: ps_out, type: \"rds\", file: \"ps_out.rds\", description: \"Phyloseq object\" },\n { name: ordination, type: \"png\", file: \"Ordination_mqc.png\", description: \"Ordination plot\" },\n { name: tax_table_biom, type: \"txt\", file: \"tax_table.qiime.txt\", description: \"Taxa table for qiime\" },\n { name: out_table_biom, type: \"biom\", file: \"otu_table.qiime.biom\", description: \"OTU table for qiime\" },\n ],\n options:\n [\n {\n name: dada2_threads,\n prefix: -t,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: dada2_no_filter_and_trim,\n prefix: ,\n type: checkbox,\n value: FALSE,\n label: \"Skip filter and trim step\",\n },\n {\n name: dada2_remove_chim,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"Remove chimeras\",\n },\n # {\n # name: dada2_marker_type,\n # type: select,\n # choices: [\n # 16S: \"16S\",\n # 18S: \"18S\",\n # ITS: \"ITS\",\n # COI: \"COI\"\n # ],\n # value: \"16S\",\n # label: \"Marker type\",\n # prompt: \"Choose unite as taxonomy source if your marker type is ITS\"\n # },\n \n {\n name: dada2_taxonomypath,\n type: select,\n choices: [\n silva138 (16S): \"\/taxonomy\/silva138\",\n silva132 (16S): \"\/taxonomy\/silva132\",\n silva128 (16S): \"\/taxonomy\/silva128\",\n rdp16 (16S): \"\/taxonomy\/rdp16\",\n greengenes13.8 (16S): \"\/taxonomy\/gg13_8\",\n unite_8.2 (ITS): \"\/taxonomy\/unite_8.2\",\n unite_2_2_2019 (ITS): \"\/taxonomy\/unite_2_2_2019\",\n midori_COI (COI): \"\/taxonomy\/midori_coi\",\n midori_COI_Without_Terrestrial (COI): \"\/taxonomy\/midori_coi_wo_terrestrial\",\n refseq-rdp16s (16S): \"\/taxonomy\/refseq-rdp16s\"\n ],\n value: \"silva138 (16S)\",\n label: \"Taxonomy source\"\n },\n # {\n # name: dada2_metadata,\n # type: input_file,\n # accept: [\".csv\",\".tsv\",\".txt\"],\n # value: \"\",\n # multiple: FALSE,\n # label: \"Metadata file\",\n # },\n {\n name: dada2_truncLen_forward,\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: 1,\n label: \"truncLen forward : Truncate reads after truncLen bases. Reads shorter than this are discarded\",\n },\n {\n name: dada2_truncLen_reverse,\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: 1,\n label: \"truncLen reverse : Truncate reads after truncLen bases. Reads shorter than this are discarded\",\n },\n {\n name: dada2_maxEE_forward,\n type: numeric,\n value: -1,\n min: -1,\n max: NA,\n step: 1,\n label: \"maxEE forward : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering).\",\n },\n {\n name: dada2_maxEE_reverse,\n type: numeric,\n value: -1,\n min: -1,\n max: NA,\n step: 1,\n label: \"maxEE reverse : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering).\",\n },\n ],\n },\n ],\n install: {\n # dada2: [\n # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"benjjneb\/dada2\\\", ref=\\\"v1.18\\\");library(\\\"dada2\\\")'\",\n # ],\n # phyloseq: [\n # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"joey711\/phyloseq\\\");library(\\\"phyloseq\\\")'\"\n # ],\n # biomformat: [\n # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"joey711\/biomformat\\\");library(\\\"biomformat\\\")'\"\n # ],\n # krona: [\n # \"cd \/opt\/biotools\",\n # \"git clone https:\/\/github.com\/marbl\/Krona.git\",\n # \"cd Krona\/KronaTools\",\n # \".\/install.pl --prefix \/opt\/biotools\",\n # \"cd \/opt\/biotools\",\n # \"rm -r Krona\/ExcelTemplate\"\n # ],\n # mbb_mqc_plugin:\n # [\n # \"cd \/opt\/biotools\",\n # \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/mmassaviol\/mbb_mqc_plugin.git\",\n # \"cd mbb_mqc_plugin\",\n # \"python3 setup.py install\"\n # ]\n },\n script: dada2.script.R,\n data: [\n {\n name: taxonomy,\n type: directory\n }\n ],\n citations: {\n dada2: [\n \"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038\/nmeth.3869\"\n ],\n phyloseq: [\n \"McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217\"\n ],\n biomformat: [\n \"Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, Volume 1, Issue 1, December 2012, 2047-217X-1-7, https:\/\/doi.org\/10.1186\/2047-217X-1-7\"\n ],\n krona: [\n \"Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385\"\n ],\n\n }\n}\n" } ]