galign SNP and Deletion Search Tools
The advent of high-throughput sequencing has allowed researchers to generate large amounts of sequence data, making whole-genome sequencing (WGS) a practical approach for gene cloning. For organisms such as Caenorhabditis elegans and Drosophila, obtaining sufficient genome coverage to sample essentially every nucleotide is readily achievable. galign is software for identifying genomic variants in C. elegans from whole-genome sequencing data.
Installation
Download the latest version of galign here. Please follow the instructions in the accompanying Readme file.
Source code is available here.
The original publication describing galign can be downloaded here.
Documentation for earlier versions, some of which remains relevant to version 1.0, is available here.
Output Files
galign compares sequencing data against the C. elegans Release 195 genome annotation and partitions candidate variants into exon, intron, and intergenic categories.
The files
csnp_exons,
csnp_intron, and
csnp_intergenic
contain the raw variant calls.
To remove background polymorphisms, these variants are compared with 25 whole-genome sequencing datasets generated in our laboratory. This produces three additional files:
- exons_txt – SNPs shared with other datasets are marked with an asterisk.
- exons_nr.txt – SNPs marked with an asterisk have been removed.
- exons_ems.txt – Coding SNPs consistent with EMS-induced mutations.
Files ending in _del contain predicted deletion sites inferred from
regions lacking sequence reads.
Additional details are available in the
publication.
In practice, we have found exons_nr.txt and the _del files to be the most useful outputs.