Seqtk protocols

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Seqtk specifications


Unique identifier OMICS_09736
Name Seqtk
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output format FASTA, FASTQ
Biological technology Illumina
Operating system Unix/Linux
Programming languages C
License MIT License
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes



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  • person_outline Vince Buffalo <>

Seqtk in pipelines

PMCID: 5752202
PMID: 29297465
DOI: 10.7554/eLife.31216.024

[…] only reads with 100% alignment to either genome were kept for further analysis and were allocated into two files according to snp mapping. each file was then converted back into fastq format using seqtk 1.0 ( and remapped with bowtie2 to the genome corresponding with its snp alignment. to adjust for the variable mapping efficiency of each snp-parsed file to either […]

PMCID: 5810276
PMID: 29472898
DOI: 10.3389/fmicb.2018.00040

[…] amplitaq gold 360 mastermix (life technologies, australia)., paired-ends reads were assembled by aligning the forward and reverse reads using pear (version 0.9.5) (). primers were trimmed using seqtk (version 1.0) and the trimmed sequences were processed using quantitative insights into microbial ecology (qiime 1.8) () usearch (version 7.1.1090) and uparse () software. using usearch […]

PMCID: 5818608
PMID: 29459752
DOI: 10.1038/s41598-018-21190-7

[…] by the fpkm value of the highest expressed gene of the same virus., 1/10 and 1/20 subsamples of pcdnv related whole transcriptome reads were randomly selected from total reads using the toolkit seqtk and analyzed using the same analytical pipeline conducted for the full transcriptomes to examine potential impact of sequencing depth., star (version 2.5.3a) was applied to check the detected […]

PMCID: 5859661
PMID: 29554982
DOI: 10.1186/s40168-018-0434-3

[…] publicly available in arrayexpress under accession e-mtab-4014 at, fastq files were quality checked using fastqc [] and illumina adapters removed with seqtk []. reads were trimmed to remove the first 14 bases, those with phred quality < 20 from the end of reads, all reads containing any n bases and those with < 100 bases post-trimming using […]

PMCID: 5863793
PMID: 29599758
DOI: 10.3389/fmicb.2018.00388

[…] were identified and annotated through the microbial genome annotation pipeline of the img online system (). raw paired-end sequences from each sample were quality controlled (trimfq command in seqtk v.1.0-r72-dirty, default settings) and mapped to cds sequences with bowtie2. cds sequences assigned to eukaryotes and viruses were excluded from analysis. cds sequences assigned […]

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Seqtk in publications

PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] checked using fastqc []. to eliminate variance in circrna detection that could arise due to differences in the number of sequencing reads, all fastq files were down-sampled to 85,547,262 reads using seqtk []. the down-sampled fastq files were then run through four different circrna prediction algorithms—circexplorer (v1.1.10), ciri (v2), find_circ (v1), and knife (v1.4), using the parameter […]

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17

[…] (). fastq sequencing output files from strains with more than 100× coverage were down-sampled using a custom script ( based on the seqtk toolkit ( antibiotic resistance phenotypes were predicted for each strain based on the methods of gordon et al. (). roary () was used to estimate a pan-genome […]

PMCID: 5920086
PMID: 29700302
DOI: 10.1038/s41467-018-04111-0

[…] cdna libraries were prepared off-site and sequencing was performed on a nextseq 500. sequencing reads were processed and analyzed using a custom pipeline. fastq files were initially trimmed using seqtk. quality of the fastq files were assessed via fastqc. trimmed reads were aligned to the mouse (mm10) genome using hisat2. htseq was utilized to obtain transcript counts for each sample, […]

PMCID: 5918799
PMID: 29694397
DOI: 10.1371/journal.pone.0195481

[…] of helminth, vertebrate and plastids hits are reported in , and tables., reads assigned to the species t. trichiura and t. muris and the ascaris genus by the lca algorithm, were extracted using seqtk version 1.0-r31 and the subseq command. reads were re-mapped to the t. trichiura sequence from humans in uganda (kt449826), the ascaris sp. sequence from haplotype 07 (pug3-1-h07) or the t. […]

PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] 1 were assembled de novo; (3) 50,000 to 100,000 quality-controlled reads from step 1 were subsampled then assembled de novo. the first pipeline combined publicly available tools: faqcs for qc [], seqtk for subsampling [] and spades (version 3.5.0) for assembly []. the second pipeline includes ngs core tools from clc genomics workbench (version 10, qiagen, redwood city, ca, usa). both faqcs […]

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