BioRuby executables is a collection of miscellaneous utilities for bioinformatics that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity, they were moved to this gem.

Parse publications for gene names in a fuzzy fashion

Interface for express beta diversity file formats

ools to work with fasta files, indexed with samtools. The initial releases depend on bio-samtools, but that will change

ruby parser for FastQC, a quality control software for high-throughput sequencing data.

bio-gag is a biogem for detecting and correcting a particular type of error that occurs/occurred in particular versions of the IonTorrent DNA sequencing kit. Recent versions of the system don't appear to suffer the same problem

Bioinformatics. Aggregate FastQC (quality control for Next Generation Sequencing -NGS-) results from many different samples in a single web page, with charts and tables organized and simplified. The main goal is to speed up the communication process with colleagues (PIs, Biologists, BioInformatic...

Ruby wrapper for the gff3-pltools.

A Ruby client for GGGenome the Ultrafast sequence search

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

A BioGem to submit jobs on a queue system

Enables programmatic parsing of HMMER version 3 reports

Parse PFAM HMM definition files so that the models can be accessible programmatically

Reads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmaticly useful state.

A Jruby wrapper to Incanter lib

BioInterchange is a Ruby gem, command-line tool, web-service for turning heterogeneous data formats such as JSON, XML, GFF3, etc., into RDF."

a programmatic interface to the iPCRess in-silico PCR software. iPCRess is part of the exonerate suite.

Basic tools for parsing, searching, and comparing JASPAR motifs; Based on Bio.motifs module in Biopython

Basic wrapper for the Kallistio Mapper

A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.