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SIMM (Simultaneous Identification of Multiple Mutations) pipeline provides a workflow to align the clean reads to reference genome, call SNPs between mutants and reference genome, then genotype the SNPs and identify causal mutations from different mutants simultaneously without the sequencing information of wild-type progenitor. Individuals with mutant homozygous phenotype are bulked and sequenced to >20X, and then analyzed with SIMM to identify causal mutation(s) responsible for the mutant phenotype. Correction of sites within candidate region is required when necessary.
SIMM has been proved to be efficiently in identifying causal mutations in rice and Arabidopsis. It can decrease the candidate SNPs to a few sites.
Features
- mutation identification
- plant
- multiple mutants
- agriculture
- bioinformatics
License
Apache License V2.0Follow SIMM
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User Reviews
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Thanks for the users sending me the bugs when using SIMM. The first version cannot deal with the genotype files generated with pileup and vcf files at the "identify" step. An updated 'filter_genotype.pl' has been uploaded. Please download it and replace it within /SIMM/bin. Please contact with me when you have problems with SIMM pipeline. The version 2.0 with multiple alignment tools (for both DNA and RNA-seq) will be updated in January.