SRST pipeline

SRST specifications


Unique identifier OMICS_12777
Alternative names Short Read Sequence Typing, SRST2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequences flanking each locus, Illumina read data
Input format FASTQ
Output data Locus variants, scores and coverage statistics for each locus and readset
Operating system Unix/Linux, Mac OS
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.2.0
Stability Stable
Requirements SAMtools, Scipy, Numpy, bowtie
Maintained Yes



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  • person_outline Kathryn Holt <>

Publications for Short Read Sequence Typing

SRST IN pipelines

PMCID: 5328445
PMID: 27974539
DOI: 10.1128/JCM.02405-16

[…] bioproject prjeb14267 at the european nucleotide archive; see table s1 in the supplemental material) were assembled using spades (18). most (19) was used to call multilocus sequence type (mlst) and srst2 (20) was used for antibiotic resistance genes. single nucleotide polymorphisms (snps) were called using bwa (21) and gatk (22) with acapsular s. pneumoniae r6 (nc_003098) used as a reference. […]

PMCID: 4979109
PMID: 27507015
DOI: 10.1186/s12864-016-2883-z

[…] [63]. quality of assemblies was verified by quast [64] and the average genome coverage was determined using samtools [65]., mlst sequence types were determined for 22 fls isolates by running srst2 v0.1.6 [66] on short read fastq.gz files, using the b. cereus allele and sequence type definition database obtained from the pubmlst database [35] using a script. unidentified […]

PMCID: 5075713
PMID: 27781166
DOI: 10.7717/peerj.2571

[…] a distance matrix and neighbor joining tree were calculated using the r phangorn package (schliep, 2010). s. aureus mlst genotypes were assigned using the srst2 (inouye et al., 2014) program running on the raw fastq files., dna fasta files of representative genomes of 25 s. aureus genome groups were downloaded in august 2015 […]

PMCID: 5075713
PMID: 27781166
DOI: 10.7717/peerj.2571

[…] groups were downloaded in august 2015 ( synthetic 5x coverage was generated for each using art(35). mlst types were ascertained using srst2(58) and binstrain subtypes were ascertained using the v2 matrix., for this study we obtained raw mwgs sequence data in fastq files for 1,265 samples from the hmp ftp site […]

PMCID: 4387542
PMID: 25904905
DOI: 10.3389/fmicb.2015.00272

[…] and trimmed as described above. allele numbers and st numbers were determined by matching the public database. the sts of sequenced strains were determined from raw short read sequences using the short read sequence typing (srst2) pipeline (inouye et al., 2012)., the extent of recombination and mutation within the population was visualized and analyzed by several approaches. the contribution […]

SRST institution(s)
Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia
SRST funding source(s)
This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant #VR0082.

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