[ { "id": "lastz", "name": "lastz", "description": "A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically", "version": "1.04.15", "website": "http:\/\/www.bx.psu.edu\/~rsharris\/lastz\/", "git": "https:\/\/github.com\/lastz\/lastz", "documentation": "http:\/\/www.bx.psu.edu\/~rsharris\/lastz\/README.lastz-1.04.03.html", "article": null, "multiqc": "custom", "commands": [ { "name": "lastz", "cname": "Lastz", "command": "lastz", "category": "blast", "output_dir": "lastz", "inputs": [ { "name": "reference_fasta", "type": "contigs" }, { "name": "contigs", "type": "fasta" } ], "outputs": [ { "name": "align_on_ref", "type": "sam", "file": "{sample}.vs_probes_default.sam", "description": "Contigs mapping on reference" } ], "options": [ { "name": "lastz_reference_fasta", "type": "input_file", "value": "", "label": "Path to reference fasta file" } ] } ], "prepare_report_script": "lastz.prepare.report.py", "prepare_report_outputs": [ "lastz_stats_mqc.csv" ], "install": [], "citations": { "lastz": [ "Zerbino, D. R., & Birney, E. (2008). lastz: algorithms for de novo short read assembly using de Bruijn graphs. Genome research, 18(5), 821-829" ], "samtools": [ "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352" ] }, "yaml": "{\n id: lastz,\n name: lastz,\n description: \"A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically\",\n version: \"1.04.15\",\n website: \"http:\/\/www.bx.psu.edu\/~rsharris\/lastz\/\",\n git: \"https:\/\/github.com\/lastz\/lastz\",\n documentation: \"http:\/\/www.bx.psu.edu\/~rsharris\/lastz\/README.lastz-1.04.03.html\",\n article: ~,\n multiqc: \"custom\",\n commands:\n [\n {\n name: lastz,\n cname: \"Lastz\",\n command: lastz,\n category: \"blast\",\n output_dir: lastz,\n inputs: [{ name: reference_fasta, type: \"contigs\" }, { name: contigs, type: \"fasta\" }],\n outputs: [\n { name: \"align_on_ref\", type: \"sam\", file: \"{sample}.vs_probes_default.sam\", description: \"Contigs mapping on reference\" }\n ],\n options:\n [\n {\n name: lastz_reference_fasta,\n type: input_file,\n value: \"\",\n label: \"Path to reference fasta file\",\n },\n ],\n },\n ],\n prepare_report_script: lastz.prepare.report.py,\n prepare_report_outputs: [\n lastz_stats_mqc.csv\n ],\n install: {\n # lastz: [\n # \"cd \/opt\/biotools\",\n # \"wget -O lastz-1.04.03.tar.gz http:\/\/www.bx.psu.edu\/~rsharris\/lastz\/lastz-1.04.03.tar.gz\",\n # \"tar -xvzf lastz-1.04.03.tar.gz\",\n # \"cd lastz-distrib-1.04.03\/src\",\n # \"make -j 10\",\n # \"mv lastz* \/opt\/biotools\/bin\/\",\n # \"cd ..\/..\",\n # \"rm -r lastz-distrib-1.04.03 lastz-1.04.03.tar.gz\"\n # ],\n # samtools: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n # \"tar -xvjf samtools-1.9.tar.bz2\",\n # \"cd samtools-1.9\",\n # \".\/configure && make\",\n # \"cd ..\",\n # \"mv samtools-1.9\/samtools bin\/samtools\",\n # \"rm -r samtools-1.9 samtools-1.9.tar.bz2\"\n # ]\n },\n citations: {\n lastz: [\n \"Zerbino, D. R., & Birney, E. (2008). lastz: algorithms for de novo short read assembly using de Bruijn graphs. Genome research, 18(5), 821-829\"\n ],\n samtools: [\n \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n ]\n }\n}\n\n# You must specify a target file\n# lastz-- Local Alignment Search Tool, blastZ-like\n# (version 1.04.03 released 20191114)\n# usage: lastz target [query] [options]\n# (common options; use --help for a more extensive list)\n# target, query specifiers or files, containing sequences to align\n# (use --help=files for more details)\n# --seed= set seed pattern (12of19, 14of22, or general pattern)\n# (default is 1110100110010101111)\n# --[no]transition allow (or don't) one transition in a seed hit\n# (by default a transition is allowed)\n# --[no]chain perform chaining\n# (by default no chaining is performed)\n# --[no]gapped perform gapped alignment (instead of gap-free)\n# (by default gapped alignment is performed)\n# --step= set step length (default is 1)\n# --strand=both search both strands\n# --strand=plus search + strand only (matching strand of query spec)\n# (by default both strands are searched)\n# --scores= read substitution and gap scores from a file\n# --xdrop= set x-drop threshold (default is 10sub[A][A])\n# --ydrop= set y-drop threshold (default is open+300extend)\n# --infer[=] infer scores from the sequences, then use them\n# all inference options are read from the control file\n# --hspthresh= set threshold for high scoring pairs (default is 3000)\n# ungapped extensions scoring lower are discarded\n# can also be a percentage or base count\n# --gappedthresh= set threshold for gapped alignments\n# gapped extensions scoring lower are discarded\n# can also be a percentage or base count\n# (default is to use same value as --hspthresh)\n# --include= read command line arguments from a text file\n# --help list \"all\" options (but the online documentation is\n# more complete)\n# --help=files list information about file specifiers\n# --help=shortcuts list blastz-compatible shortcuts\n# --help=defaults list scoring defaults for your current settings\n# --help=yasra list yasra-specific shortcuts\n\n# See the online documentation at http:\/\/www.bx.psu.edu\/~rsharris\/lastz for\n# the most up-to-date information.\n" } ]