ABRA: improved coding indel detection via assembly-based realignment

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

(2014) Matthew D. Wilkerson et al.   NUCLEIC ACIDS RESEARCH

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads

(2011) Paolo Carnevali et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

(2010) Nils Homer et al.   GENOME BIOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS