SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Publication Date
October 05, 2016
Journal
PLOS ONE
Authors
Wei Shen, Shuai Le, Yan Li & Fuquan Hu
Volume
11
Issue
10
Pages
e0163962
DOI
https://dx.plos.org/10.1371/journal.pone.0163962
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0163962
Scopus
84992166172
Mendeley
http://www.mendeley.com/research/seqkit-crossplatform-ultrafast-toolkit-fastaq-file-manipulation
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Mendeley | Further Information

{"title"=>"SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", "type"=>"journal", "authors"=>[{"first_name"=>"Wei", "last_name"=>"Shen", "scopus_author_id"=>"55574196327"}, {"first_name"=>"Shuai", "last_name"=>"Le", "scopus_author_id"=>"55553195400"}, {"first_name"=>"Yan", "last_name"=>"Li", "scopus_author_id"=>"57190386888"}, {"first_name"=>"Fuquan", "last_name"=>"Hu", "scopus_author_id"=>"7202525462"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"27706213", "doi"=>"10.1371/journal.pone.0163962", "sgr"=>"84992166172", "scopus"=>"2-s2.0-84992166172", "issn"=>"19326203", "pui"=>"612643999"}, "id"=>"09764058-e020-388a-8506-163ad6ec6b96", "abstract"=>"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 paper 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 OSX, 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. SeqKit is open source and available on Github at https://github.com/shenwei356/seqkit.\\r\\n\\r\\n", "link"=>"http://www.mendeley.com/research/seqkit-crossplatform-ultrafast-toolkit-fastaq-file-manipulation", "reader_count"=>51, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>17, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>12, "Student > Master"=>9, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>17, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>12, "Student > Master"=>9, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>15, "Agricultural and Biological Sciences"=>24, "Computer Science"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>7}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Austria"=>1, "United States"=>1, "China"=>2, "Denmark"=>1}, "group_count"=>1}

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