bio-ngs provides a framework for handling NGS data with BioRuby

bio-ngs provides a framework for handling NGS data with BioRuby

Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat

A parser for CIGAR format alignments.

BioRuby plugins with dependecies from external library or tools

Identify causative mutations in a model genome from NGS reads using the NGM method.

Identify causative mutations in a model genome from NGS reads using the NGM method.

Iterate through a samtools pileup file

Simple classes for parsing SAM, CIGAR and MD:Z strings, including slices. Methods for calling mutations in HGVS format and looking up consequences using Ensembl VEP REST API. Developed for calling mutations at an expected position in an alignment - e.g. Amplicon sequencing of CRISPR-induced mutations.

A minimal web service on the top of sinatra to query bam files

a library and commandline tool to pick causative mutation from bulks segregant sequencing

Calculated a metric that estimates read complexity at each base for RNA-seq BAM files. Alternative to pileup format.

A variance calling tool for NGS

A variance calling tool for NGS