SNP-o-matic statistics

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SNP-o-matic specifications


Unique identifier OMICS_15114
Name SNP-o-matic
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input data The reference genome sequence, the sequence reads, a list of putative SNPs.
Input format FASTA, FASTQ
Output data The predicted mapping/alignment.
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Heinrich Magnus Manske <>

Publication for SNP-o-matic



2009 Bioinformatics
PMCID: 2735664
PMID: 19574284
DOI: 10.1093/bioinformatics/btp403

SNP-o-matic in publications

PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] 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 (, for genomes that are smaller or bigger than 100 mb, respectively. the software analyzes the assembly base-per-base […]

PMCID: 4786412
PMID: 26943619
DOI: 10.7554/eLife.08714.030

[…] ogram () ( 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 […]

PMCID: 3738909
PMID: 22722859
DOI: 10.1038/nature11174

[…] 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., […]

PMCID: 3138765
PMID: 21789235
DOI: 10.1371/journal.pone.0022213

[…] 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 […]

PMCID: 3218861
PMID: 21477297
DOI: 10.1186/gb-2011-12-4-r35

[…] 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 […]

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SNP-o-matic institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
SNP-o-matic funding source(s)
This work was supported by the Wellcome Trust, Bill and Melinda Gates Foundation and Medical Research Council.

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