Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

(2015) Koen Herten et al.   BMC BIOINFORMATICS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Dissemination of scientific software with Galaxy ToolShed

(2014) Daniel Blankenberg et al.   GENOME BIOLOGY

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

(2013) Paul Igor Costea et al.   PLoS One

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS