CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

(2011) Yi Zheng et al.   BMC BIOINFORMATICS

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species

(2011) Andrea Bräutigam et al.   JOURNAL OF EXPERIMENTAL BOTANY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach

(2010) Christoph Mayer et al.   BMC GENOMICS

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome Projector: zoomable genome map with multiple views

(2009) Kazuharu Arakawa et al.   BMC BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH