Seqtk pipeline

Seqtk specifications

Information


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
Operating system Unix/Linux
Programming languages C
License MIT License
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Vince Buffalo <>

Seqtk IN pipelines

 (10)
2018
PMCID: 5752202
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 (https://github.com/lh3/seqtk) 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 […]

2018
PMCID: 5863793
PMID: 29599758
DOI: 10.3389/fmicb.2018.00388

[…] and annotated through the microbial genome annotation pipeline of the img online system (chen et al., 2016). 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 […]

2017
PMCID: 5407278
PMID: 28462059
DOI: 10.7717/peerj.3269

[…] (bolger, lohse & usadel, 2014). each library was assembled into contigs using 17,000,000 reads and idba-ud (peng et al., 2012), and normalized to the smallest library size (6,000 contigs) using seqtk (https://github.com/lh3/seqtk) (perner et al., 2014) (table s1 ). all contigs were searched against the ncbi nt database using blast and analyzed in megan (huson et al., 2007), requiring […]

2017
PMCID: 5414317
PMID: 28464948
DOI: 10.1186/s13059-017-1209-z

[…] bbmap package (v35.10; b. bushnell, http://sourceforge.net/projects/bbmap/). the first 11 and the last six nucleotides of every read were further removed with seqtk (h. li, https://github.com/lh3/seqtk). finally, reads shorter than 50 bp were removed with trimmomatic (v0.33) [81]., we extracted dna with the nucleomag® 96 plant (macherey-nagel) kit according to the manufacturer’s instructions. […]

2017
PMCID: 5462746
PMID: 28592799
DOI: 10.1038/s41598-017-03020-4

[…] carried out on an illumina hiseq 2500 system according to the manufacturer’s instructions (illumina hiseq 2500 user guide) and 150-bp paired-end reads were obtained. the raw reads were filtered by seqtk and then mapped to the m. marinum m strain reference sequence (genbank gca_000018345.1) using bowtie2 (version: 2–2.0.5)60. counting of reads per gene was performed using htseq followed by tmm […]

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