New Sambamba library comes with a command-line tool for working with SAM/BAM files. This gem brings some of its functionality to Ruby.

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

Entries in a flatfile will be parased by the BioRuby's Bio::FlatFile.auto module. These entries are used as queries for the Sun Grid Engine (SGE) system. Huge amount of queries are automatically splitted into subdirectories. With a specified command line to be executed, queries are submited to the SGE as an array job.

A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least.

A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.

Parses stockholm sequence alignment format

Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation.

Tabix file indexing routines from the samtools package http://samtools.sourceforge.net/

A bioruby plugin for interaction with the transmembrane predictor TMHMM

Ruby FFI binding of the ucsc kent src. Implemented utilities include: bigWigInfo, bigWigSummary and wigToBigWig

BioRuby plugin for UniChem REST Web service

Parser to work with some file formats used in the velvet DNA assembler

Bindings to some internals of the velvet assembler.

Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/

bipbop is the best service for consulting brazilian data. See http://bipbop.com.br/ for more information.

IRB with added functions to require, load and reload files faster

Mostly drop-in replacement for Logger with a more robust log rotation facility

Ruby wrapper for bishl.de xml api.

Bisque exists to ease the organizational pain of having to attach reporting and ad-hoc queries to ActiveRecord models in order to get any class-like behavior out of them by providing a new class and DSL for that express purpose.