Sequence manipulation toolbox

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Sequence editing and filtering tools

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various tools

  • bioAwk - an addition to the already fantastic AWK to handle biological sequences (by Heng Li)
  • seqtk - a sequence tool-kit to manipulate and filter sequences (by Heng Li)
  • seq_crumbs - a collection of small sequence processing utilities (biopython)
  • readsdeq GUI - A java GUI to convert bio sequence format (old but good!)
  • ngsutils - A series of 50+ dedicated toolboxes to manipulate data, including: bamutils (BAM/SAM files), bedutils (BED files), fastqutils (FASTQ files, base- and color-space), gtfutils (GTF gene models) (python)
  • ea-utils - Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.
  • biotoolbox - perl scripts to call in bash to process data in various ways (depends on a built kent code)
  • Kent utilities and source tree - Unmissable utilities used by the UCSC browser and many more.


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