Bioinformatics · Command Line Utilities

Command Line Utilities

• wireservice/csvkit on GitHub, opens in a new tab

  6.4Kstars

  Utilities for working with CSV/Tab-delimited files. [ web ]

  Python·MIT License·active·2 weeks ago

• stephenturner/oneliners on GitHub, opens in a new tab

  2Kstars

  Git repo of useful single line commands.

  slowing·3 years ago

• shenwei356/csvtk on GitHub, opens in a new tab

  1.2Kstars

  Another cross-platform, efficient, practical and pretty CSV/TSV toolkit. [ web ]

  Go·MIT License·active·3 weeks ago

• mattgodbolt/zindex on GitHub, opens in a new tab

  659stars

  Create an index on a compressed text file.

  C·BSD 2-Clause "Simplified" License·dormant·4 years ago

• bionode/bionode on GitHub, opens in a new tab

  313stars

  Modular and universal bioinformatics, Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatics analysis workflows. [ web ]

  JavaScript·MIT License·steady·3 months agoarchived

• bioSyntax/bioSyntax on GitHub, opens in a new tab

  273stars

  Syntax Highlighting for Computational Biology file formats (SAM, VCF, GTF, FASTA, PDB, etc...) in vim/less/gedit/sublime. [ paper-2018 | web ]

  Shell·GNU General Public License v3.0·dormant·3 years ago

• samtools/tabix on GitHub, opens in a new tab

  92stars

  Table file index. [ paper-2011 ]

  C·dormant·5 years agoarchived

• arq5x/grabix on GitHub, opens in a new tab

  86stars

  A wee tool for random access into BGZF files.

  C·MIT License·dormant·8 years ago

• Rbfinch/grepq on GitHub, opens in a new tab

  60stars

  Fast FASTQ filtering by matching reads against one or more regex patterns.

  Rust·MIT License·steady·4 months ago

• brentp/gsort on GitHub, opens in a new tab

  36stars

  Sort genomic files according to a specified order.

  Go·MIT License·steady·9 months ago

• shenwei356/easy_qsub on GitHub, opens in a new tab

  29stars

  Easily submitting PBS jobs with script template. Multiple input files supported.

  Python·MIT License·dormant·3 years ago

• wormtable/wormtable on GitHub, opens in a new tab

  27stars

  Write-once-read-many table for large datasets.

  Python·GNU Lesser General Public License v3.0·slowing·3 years ago