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SRST README 25 Sep, 2013 This project has now been replaced by SRST2 - Short Read Sequence Typing for Bacterial Pathogens, available at http://katholt.github.io/srst2/ The new SRST2 program does gene typing as well as MLST (e.g. typing resistance genes, virulence genes, etc). SRST2 is faster and more accurate than the old SRST, using bowtie2 to achieve local alignments (no need for flanking sequences) and a brand new scoring system. LEGACY README ------------------ SRST uses bwa, samtools and a novel scoring system to determine the multi-locus sequence type (ST) for bacterial sequencing projects direct from Illumina reads. See the instructions (PDF) for usage instructions and dependencies. You need to use prepSRST.py before you can use srst.py. ----------------------- SRST Latest update: 30/5/2013. - Fixed a problem where the ordering of locus names in the output file was sometimes wrong (if the order of loci in the profiles file was not alphabetical). This resulted in loci being combined in the wrong order and thus STs being called incorrectly. Previous update: 4/8/2012. - Serious bug fix, update to this version is required to fix error at line 527 ----------------------- Note an additional script, mlstBLAST, is also available for extracting STs from assembled sequence data. Script and readme are available in the mlstBLAST folder.