Difference between revisions of "Srst2"
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srst2 --input_pe ERR024070*.fastq.gz --output shigella1 --log --save_scores --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --gene_db ARGannot.fasta | srst2 --input_pe ERR024070*.fastq.gz --output shigella1 --log --save_scores --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --gene_db ARGannot.fasta | ||
| − | + | Note particularly how two databses are specified here. | |
| − | * '''--mlst_db''' this is for specifying the database, usually a fasta file. | + | |
| + | * '''--mlst_db''' this is for specifying the MLST database, usually a fasta file with the allele sequences for certain marker sequences. In srst2 this will be the concatenated fasta of different versions of the 7 housekeeping genes which correspond to the different allele sequences of the gene. | ||
Revision as of 14:22, 28 April 2016
Introduction
This python based tool with two main dependencies (samtools and bowtie2) carries out mapping of short reads to detect overall three targets:
- genes
- alleles
- multi-locus sequence types (MLST)
from WGS data (which we can take to be NGS short reads).
A smaller number of loci, i.e. 7, are used to divide the population.
These loci come in the shape of entire housekeeping genes that all the species and isolates are bound to have.
This proves to be robust unlike the alternative of assembling the genomes de-novo, which, when dealing with 100 or 1000 bacterial genomes (a typical workload in bacteria), is a major issue.
Example command lines
srst2 --input_pe ERR024070*.fastq.gz --output shigella1 --log --save_scores --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --gene_db ARGannot.fasta
Note particularly how two databses are specified here.
- --mlst_db this is for specifying the MLST database, usually a fasta file with the allele sequences for certain marker sequences. In srst2 this will be the concatenated fasta of different versions of the 7 housekeeping genes which correspond to the different allele sequences of the gene.
Glossary
- ST: sequence type ... usually a category a certain sequence can be said to belong to.
- MLST: MultiLocus Sequence Type
