Sequence manipulation toolbox
From BITS wiki
- 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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