{"id":25977613,"url":"https://github.com/nylander/consensus-sequence","last_synced_at":"2026-04-20T14:33:52.948Z","repository":{"id":195821716,"uuid":"185575814","full_name":"nylander/consensus-sequence","owner":"nylander","description":null,"archived":false,"fork":false,"pushed_at":"2023-09-19T15:24:11.000Z","size":16,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2023-09-19T19:09:33.646Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nylander.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-05-08T09:34:27.000Z","updated_at":"2023-09-19T19:09:40.917Z","dependencies_parsed_at":"2023-09-19T19:23:55.853Z","dependency_job_id":null,"html_url":"https://github.com/nylander/consensus-sequence","commit_stats":null,"previous_names":["nylander/consensus-sequence"],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fconsensus-sequence","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fconsensus-sequence/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fconsensus-sequence/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fconsensus-sequence/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nylander","download_url":"https://codeload.github.com/nylander/consensus-sequence/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241966988,"owners_count":20050324,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-05T04:38:43.729Z","updated_at":"2026-04-20T14:33:47.925Z","avatar_url":"https://github.com/nylander.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Calculate consensus sequence from fasta or CSV\n\n- Last modified: tis sep 19, 2023  05:23\n- Sign: JN\n\n## Description\n\nTwo scripts for calculating consensus or compromise (DNA) sequences from either fasta or csv input format.\n\n\n### consensus-seq.pl\n\n            FILE: consensus-seq.pl\n\n           USAGE: ./consensus-seq.pl fasta-alignment-file\n\n     DESCRIPTION: Calculate consensus sequence from fasta alignment.\n                  Can use a consensus level (1-100), or represent\n                  a (strict) consensus using IUPAC symbols.\n\n                  Prints to STDOUT or, if --outfile is used, to\n                  an outfile.\n\n                  Fasta sequence is wrapped to width set by -w,\n                  (default 80), unless --nowrap is used.\n\n                  Default fasta header will be based on infile\n                  name, and will display some extra information.\n                  For example:\n\n                  \u003ein.fas|consensus [conlevel=100 nseq=8 length=3844 identity=88.93]\n\n                  The header can be overridden by using -l.\n\n                  Regarding consensus level (taken from Bio::Align::AlignI):\n\n                  \"The consensus residue has to appear at least threshold %\n                  of the sequences at a given location, otherwise a '?'\n                  character will be placed at that location.\"\n\n         OPTIONS: -i,--infile=\u003cfile\u003e  Provide fasta formatted\n                                      sequence alignment\n                  -o,--oufile=\u003cfile\u003e  Provide output file name\n                                      (will be fasta format)\n                  -c,--conlevel=\u003cnr\u003e  Provide consensus level (1-100).\n                                      Default '50'.\n                  -s,--strict         Synonym for -c=100. Overrides\n                                      -c.\n                  -l,--label=\u003cstring\u003e Provide custom fasta header.\n                  -w,--wrap=\u003cnr\u003e      Set max line length in sequence\n                                      to \u003cnr\u003e. Default is 80.\n                  -n,--nowrap         Do not wrap (interleave)\n                                      sequence string.\n                  -I,--IUPAC          Represent all ambiguities as \n                                      IUPAC symbols in the (strict)\n                                      consensus.\n\n    REQUIREMENTS: BioPerl, perldoc\n\n           NOTES: ---\n\n          AUTHOR: Johan Nylander\n\n         COMPANY: NRM\n\n         VERSION: 1.0\n\n         CREATED: 2019-09-25 09:42:04\n\n        REVISION: ---\n\n         LICENSE: MIT\n\n### consensus-seq-from-csv.pl\n\n            FILE: consensus-seq-from-csv.pl\n\n           USAGE: ./consensus-seq-from-csv.pl R84150_2009.duplicates.csv\n                  ./consensus-seq-from-csv.pl -d  R84150_2009.duplicates.csv\n                  ./consensus-seq-from-csv.pl -s ';' R84150_2009.duplicates.txt\n                  ./consensus-seq-from-csv.pl -s ';' -d  -nu dna.duplicates.txt\n\n     DESCRIPTION: Read csv file and print \"conservative consensus\".\n                  That is, if there are polymorphism in a site, a question mark\n                  is printed.\n                  Reads a file, prints to stdout.\n\n         OPTIONS: -d, --debug      Will show the input sequences and consensus aligned.\n                  -s, --separator  Define input (and output) separator (default ',').\n                  -m, --missing    Define consensus symbol. Default '?'.\n                  -n, --nucleotide Input are nucleotides. Will accept IUPAC ambiquity\n                                   symbols.\n                  -l, --label      Sequence label. If empty, will try to use file name.\n                  -f, --fasta      Input is fasta.\n                  -h, --help       Will show brief help text\n\n    REQUIREMENTS: ---\n\n           NOTES: Uses the first part of the filename (\u003cname\u003e.duplicates.txt) as \n                  output sequence name, unless given as arg.\n\n           TODO:  * Support fasta input\n                  * Support AA input\n\n          AUTHOR: Johan Nylander\n\n         COMPANY: NRM\n\n         VERSION: 1.0\n\n         CREATED: 03/12/2019 11:02:49 AM\n\n        REVISION: ---\n\n         LICENSE: MIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fconsensus-sequence","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnylander%2Fconsensus-sequence","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fconsensus-sequence/lists"}