ShoRAH

Application data
Biological application domain(s)	Metagenomics
Principal bioinformatics method(s)	Haplotype inference, Read mapping
Technology	454, Illumina
Created at	ETH Zurich
Maintained?	Yes
Input format(s)	FASTA, MSA
Software libraries	Biopython, GSL, needle
Licence	GPLv3
Operating system(s)	Linux, Mac OS X

Summary: Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

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Links

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References

1. . 2010. Nucleic Acids Research

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