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 macOS, 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.
| 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 | Yes | -- | |
| Filtering by size | Yes | 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.
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 100SeqKit version: v0.3.1.1
FASTA:
FASTQ:
We thank Lei Zhang for testing 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.