SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Documents: http://bioinf.shenwei.me/seqkit (Usage, Tutorial, Benchmark and Development Notes)

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

Latest version:

Introduction

FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly.

This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.

Features

Cross-platform (Linux/Windows/Mac OS X/OpenBSD/FreeBSD, see download)
Light weight and out-of-the-box, no dependencies, no compilation, no configuration (see download)
UltraFast (see benchmark), multiple-CPUs supported.
Practical functions supported by 20 subcommands (see subcommands and usage )
Well documented (detailed usage and benchmark )
Seamlessly parses both FASTA and FASTQ formats
Support STDIN and gziped input/output file, easy being used in pipe
Support custom sequence ID regular expression (especially useful for searching with ID list)
Reproducible results (configurable rand seed in sample and shuffle)
Well organized source code, friendly to use and easy to extend.

Features comparison

Categories	Features	seqkit	fasta_utilities	fastx_toolkit	pyfaidx	seqmagick	seqtk
Formats support	Multi-line FASTA	Yes	Yes	--	Yes	Yes	Yes

                |FASTQ                  |Yes     |Yes            |Yes          |--     |Yes      |Yes
                |Multi-line  FASTQ      |Yes     |Yes            |--           |--     |Yes      |Yes
                |Validating sequences   |Yes     |--             |Yes          |Yes    |--       |--
                |Supporting RNA         |Yes     |Yes            |--           |--     |Yes      |Yes

Functions |Searching by motifs |Yes |Yes |-- |-- |Yes |-- |Sampling |Yes |-- |-- |-- |Yes |Yes |Extracting sub-sequence|Yes |Yes |-- |Yes |Yes |Yes |Removing duplicates |Yes |-- |-- |-- |Partly |-- |Splitting |Yes |Yes |-- |Partly |-- |-- |Splitting by seq |Yes |-- |Yes |Yes |-- |-- |Shuffling |Yes |-- |-- |-- |-- |-- |Sorting |Yes |Yes |-- |-- |Yes |-- |Locating motifs |Yes |-- |-- |-- |-- |-- |Common sequences |Yes |-- |-- |-- |-- |-- |Cleaning bases |Yes |Yes |Yes |Yes |-- |-- |Transcription |Yes |Yes |Yes |Yes |Yes |Yes |Translation |-- |Yes |Yes |Yes |Yes |-- |Filtering by size |Indirect|Yes |-- |Yes |Yes |-- |Renaming header |Yes |Yes |-- |-- |Yes |Yes Other features |Cross-platform |Yes |Partly |Partly |Yes |Yes |Yes |Reading STDIN |Yes |Yes |Yes |-- |Yes |Yes |Reading gzipped file |Yes |Yes |-- |-- |Yes |Yes |Writing gzip file |Yes |-- |-- |-- |Yes |--

Note 1: See version information of the softwares.

Note 2: See usage for detailed options of seqkit.

Installation

Go to Download Page for more download options and changelogs.

SeqKit is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Just download compressed executable file of your operating system, and uncompress it with tar -zxvf *.tar.gz command or other tools. And then:

For Linux-like systems
1. If you have root privilege simply copy it to /usr/local/bin:
```
 sudo cp seqkit /usr/local/bin/
```
2. Or add the current directory of the executable file to environment variable PATH:
```
 echo export PATH=\$PATH:\"$(pwd)\" >> ~/.bashrc
 source ~/.bashrc
```
For windows, just copy seqkit.exe to C:\WINDOWS\system32.

For Go developer, just one command:

go get -u github.com/shenwei356/seqkit/seqkit

Subcommands

20 subcommands in total.

Sequence and subsequence

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

Format conversion

fx2tab covert FASTA/Q to tabular format (and length/GC content/GC skew)
tab2fx covert tabular format to FASTA/Q format
fq2fa covert FASTQ to FASTA

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
head print first N FASTA/Q records

Edit

replace replace name/sequence by regular expression
rename rename duplicated IDs

Ordering

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

Misc

version print version information and check for update

Technical details and guides for use

FASTA/Q format parsing

SeqKit uses author's lightweight and high-performance bioinformatics packages bio for FASTA/Q parsing, which has high performance close to the famous C lib klib (kseq.h).

Sequence formats and types

SeqKit seamlessly support FASTA and FASTQ format. Sequence format is automatically detected. All subcommands except for faidx can handle both formats. And only when some commands (subseq, split, sort and shuffle) which utilise FASTA index to improve perfrmance for large files in two pass mode (by flag --two-pass), only FASTA format is supported.

Sequence type (DNA/RNA/Protein) is automatically detected by leading subsequences of the first sequences in file or STDIN. The length of the leading subsequences is configurable by global flag --alphabet-guess-seq-length with default value of 10000. If length of the sequences is less than that, whole sequences will be checked.

Sequence ID

By default, most softwares, including seqkit, take the leading non-space letters as sequence identifier (ID). For example,

FASTA header	ID
>123456 gene name	123456
>longname	longname
>gi\|110645304\|ref\|NC_002516.2\| Pseudomona	gi\|110645304\|ref\|NC_002516.2\|

But for some sequences from NCBI, e.g. >gi|110645304|ref|NC_002516.2| Pseudomona, the ID is NC_002516.2. In this case, we could set sequence ID parsing regular expression by global flag --id-regexp "\|([^\|]+)\| " or just use flag --id-ncbi. If you want the gi number, then use --id-regexp "^gi\|([^\|]+)\|".

FASTA index

For some commands, including subseq, split, sort and shuffle, when input files are (plain or gzipped) FASTA files, FASTA index would be optional used for rapid access of sequences and reducing memory occupation.

ATTENTION: the .seqkit.fai file created by SeqKit is slightly different from .fai file created by samtools. SeqKit uses full sequence head instead of just ID as key.

Parallelization of CPU intensive jobs

The validation of sequences bases and complement process of sequences are parallelized for large sequences.

Parsing of line-based files, including BED/GFF file and ID list file are also parallelized.

The Parallelization is implemented by multiple goroutines in golang which are similar to but much lighter weight than threads. The concurrency number is configurable with global flag -j or --threads (default value: 1 for single-CPU PC, 2 for others).

Memory occupation

Most of the subcommands do not read whole FASTA/Q records in to memory, including stat, fq2fa, fx2tab, tab2fx, grep, locate, replace, seq, sliding, subseq.

Note that when using subseq --gtf | --bed, if the GTF/BED files are too big, the memory usage will increase. You could use --chr to specify chromesomes and --feature to limit features.

Some subcommands need to store sequences or heads in memory, but there are strategy to reduce memory occupation, including rmdup and common. When comparing with sequences, MD5 digest could be used to replace sequence by flag -m (--md5).

Some subcommands could either read all records or read the files twice by flag -2 (--two-pass), including sample, split, shuffle and sort. They use FASTA index for rapid acccess of sequences and reducing memory occupation.

Reproducibility

Subcommands sample and shuffle use random function, random seed could be given by flag -s (--rand-seed). This makes sure that sampling result could be reproduced in different environments with same random seed.

Usage && Examples

Usage and examples

Tutorial

Benchmark

More details: http://bioinf.shenwei.me/seqkit/benchmark/

Datasets:

$ seqkit stat *.fa
file          format  type   num_seqs        sum_len  min_len       avg_len      max_len
dataset_A.fa  FASTA   DNA      67,748  2,807,643,808       56      41,442.5    5,976,145
dataset_B.fa  FASTA   DNA         194  3,099,750,718      970  15,978,096.5  248,956,422
dataset_C.fq  FASTQ   DNA   9,186,045    918,604,500      100           100          100

SeqKit version: v0.3.1.1

FASTA:

FASTQ:

Citation

W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.

Acknowledgements

We thank Lei Zhang for testing of SeqKit, and also thank Jim Hester, author of fasta_utilities, for advice on early performance improvements of for FASTA parsing and Brian Bushnell, author of BBMaps, for advice on naming SeqKit and adding accuracy evaluation in benchmarks. We also thank Nicholas C. Wu from the Scripps Research Institute, USA for commenting on the manuscript and Guangchuang Yu from State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HK for advice on the manuscript.

We thank Li Peng for reporting many bugs.

Contact

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

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

License

MIT License

lindechun/seqkit