seqkit

README

fakit - Swiss army knife of FASTA format

Documents : http://shenwei356.github.io/fakit

Source code: https://github.com/shenwei356/fakit

Introduction

Features

• Cross-platform (Linux/Windows/Mac OS X/OpenBSD/FreeBSD, see download)
• Out-of-the-box, no dependencies, without compilation, light weight (see download)
• Fast (see benchmark), multiple-threads supported, more significant speedup for grep and locate.
• Practical functions by 14 subcommands (see subcommands and usage )
• Well documented (detailed usage and benchmark )
• Support STDIN and gziped input/output file, could be used in pipe
• Support custom sequence ID regular expression (especially useful for quering with ID list)
• Reproducible results (configurable rand seed in sample and shuffle)
• Well organized source code, friendly to use and easy to extend.

Subcommands

Sequence and subsequence

• seq transform sequences (revserse, complement, extract ID...)
• subseq get subsequences by region/gtf/bed, including flanking sequences
• sliding sliding sequences, circle genome supported
• stat simple statistics of FASTA files

Format conversion

• fa2tab covert FASTA to tabular format (and length/GC content/GC skew) to filter and sort
• tab2fa covert tabular format to FASTA format

Searching

• grep search sequences by pattern(s) of name or sequence motifs
• locate locate subsequences/motifs

Set operations

• rmdup remove duplicated sequences by id/name/sequence
• common find common sequences of multiple files by id/name/sequence
• split split sequences into files by id/seq region/size/parts
• sample sample sequences by number or proportion

Ordering

• shuffle shuffle sequences
• sort sort sequences by id/name/sequence

Global Flags

    --alphabet-guess-seq-length int   length of sequence prefix of the first FASTA record based on which fakit guess the sequence type (default 10000)
-c, --chunk-size int                  chunk size (attention: unit is FASTA records not lines) (default 1000)
    --id-regexp string                regular expression for parsing ID (default "^([^\\s]+)\\s?")
-w, --line-width int                  line width (0 for no wrap) (default 60)
-o, --out-file string                 out file ("-" for stdout, suffix .gz for gzipped out) (default "-")
    --quiet                           be quiet and do not show extra information
-t, --seq-type string                 sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence) (default "auto")
-j, --threads int                     number of CPUs. (default value depends on your device) (default 4)

Usage && Examples

http://shenwei356.github.io/fakit/usage/

Benchmark

http://shenwei356.github.io/fakit/benchmark/

Contact

Email me for any problem when using fakit. shenwei356(at)gmail.com

Create an issue to report bugs, propose new functions or ask for help.

License

MIT License