GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

BioJava: an open-source framework for bioinformatics in 2012

(2012) A. Prlic et al.   BIOINFORMATICS

ParsEval: parallel comparison and analysis of gene structure annotations

(2012) Daniel S Standage et al.   BMC BIOINFORMATICS

Readjoiner: a fast and memory efficient string graph-based sequence assembler

(2012) Giorgio Gonnella et al.   BMC BIOINFORMATICS

Ten Simple Rules for the Open Development of Scientific Software

(2012) Andreas Prlić et al.   PLoS Computational Biology

LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

(2012) Sascha Steinbiss et al.   Mobile DNA

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Community-driven computational biology with Debian Linux

(2011) Steffen Möller et al.   BMC BIOINFORMATICS

A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences

(2011) Sascha Steinbiss et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A standard variation file format for human genome sequences

(2010) Martin G Reese et al.   GENOME BIOLOGY

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

AnnotationSketch: a genome annotation drawing library

(2008) Sascha Steinbiss et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS