Computational protocol: Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error

Similar protocols

Protocol publication

[…] In order to ensure that only the highest quality data was used for assembly, reads were trimmed and filtered with PoPoolation set to a minimum length of 50 bp and a quality score threshold of 20. Global mapping of reads was then performed with each of four reference-guided short-read sequence assemblers: Burrows-Wheeler aligner v0.6.1-r104, MOSAIK v2.1 (code.google.com/p/mosaik-aligner/), Novoalign v3.00.03 (novocraft.com/main/index.php), and SMALT v0.7.4 (sanger.ac.uk/resources/software/smalt/). We used the Genome Analysis Toolkit [] to perform local realignments around indels according to GATK best practices []. Single nucleotide polymorphisms were then identified with BCFtools (BCF) [], FreeBayes [], the UnifiedGenotyper (UGT; https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php), and VarScan [, ]. […]

Pipeline specifications

Software tools PoPoolation, BWA, MOSAIK, NovoAlign, SMALT, GATK, bcftools, FreeBayes, VarScan
Application Pool-seq analysis
Organisms Listeria monocytogenes