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Pipeline publication

[…] hexB transformant DNA. This scheme is summarised in ., Illumina data from transformants were independently mapped to the corrected genomes of 23F-R and TIGR4Δcps using SMALT . The de novo identification of SNPs, to check for mutations not derived from imports of the donor sequence, was performed by identifying polymorphisms relative to the recipient genome as described in Harris et al. . All strains had a mean sequence read coverage of at least 20 fold, with the mean coverage across the dataset of 123 fold, for strains sequenced using the Genome Analyzer II, and 506 fold, for strains sequenced using the HiSeq., To identify RSSs, only marker SNP sites were analysed. The alignment produced by SMALT was processed using samtools and vcftools to produce Variant Call Format (VCF) outputs for each strain. Within these VCFs, all homozygous marker sites with a base quality greater than 50 were used to identify sequence characteristic of the donor or recipient in the transformation experiment. Recombinations were initially defined as regions containing donor alleles at polymorphic sites with no intervening recipient alleles. To exclude false positives, putative recombinations were rejected unless there was evidence of the transfer of at least one of the supporting marker sites from the reciprocal mapping to the donor sequence, similar to the method described by Mell et al. . The ambiguous boundary regions around each recombi […]

Pipeline specifications

Software tools SMALT, SAMtools, VCFtools