SNP-o-matic

[…] paired reads) (): takes as input a fasta file containing the scaffolds and a bam file generated by the remapping of the reads used in the assembly. first, a coverage analysis is performed using snp-o-matic () or smalt (https://www.sanger.ac.uk/resources/software/smalt), for genomes that are smaller or bigger than 100 mb, respectively. the software analyzes the assembly base-per-base […]

[…] ogram () (http://bio-bwa.sourceforge.net/) as previously described (), to identify an initial global set of 4,305,957 potential snps. this list was then used to guide stringent re-alignment using the snp-o-matic algorithm (), to reduce misalignment errors. the stringent alignments were then examined by a series of quality filters, with the aim of removing alignment artefacts and their sources. in […]

[…] 26) were determined from analyses of the snp distributions, as was the effect of applying the filters (see for details). to reduce false positives, we realigned each sample using the stringent snp-o-matic algorithm , applying a base quality score threshold of 27 and only allowing variations listed in the potential snps catalogue. the catalogue was thus reduced to 975,935 potential snps., […]

[…] samples sequenced later in time had 76 bp sequence reads. up to 3 lanes were sequenced per sample. sequence data was mapped to the reference p. falciparum genome (3d7 version 4.1.2) using the snp-o-matic read mapping tool under the parameters for perfect read matching (with allowance for pre-identified snps) (manske et al., in preparation). only sequences which mapped uniquely within […]

[…] requiring at least 95% of the probe length with less than four mismatched/indel positions excluding the central nucleotide. illumina sequence data were aligned to the 3d7 reference genome with snp-o-matic software [] to identify snp locations for comparison to microarray data., data for hb3 and dd2 (n = 6 and n = 4, respectively) hybridized against 3d7 were extracted from scanned images […]