Tag: Breakpoints

CREST 1.0.1 – uses the soft-clipped reads to directly Map the Breakpoints of SVs

CREST 1.0.1

:: DESCRIPTION

CREST (clipping reveals structure) is an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CREST

:: MORE INFORMATION

Citation

Jianmin Wang et al.
CREST maps somatic structural variation in cancer genomes with base-pair resolution
Nature Methods 8, 652–654 (2011)

SplazerS 1.1 – Detect Genomic Indel Variants with exact Breakpoints in Single- and Paired-end Sequencing

SplazerS 1.1

:: DESCRIPTION

SplazerS (Split Read Mapping as a branch of RazerS) is a tool for mapping reads containing structural variants, implemented in the highly efficient SeqAn C++ software library. SplazerS employs “split” read mapping, where prefix and suffix match of a read may be interrupted by a longer gap. This split read mapping is useful in the context of mRNA sequencing, where introns cause so-called junction reads that span exon-exon boundaries, or for the detection of small to medium-sized insertions and deletions in genomic data.

::DEVELOPER

 Anne-Katrin Emde, David Weese, Marcel Schulz, Stefan Haas, and Knut Reinert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows

:: DOWNLOAD

 SplazerS

:: MORE INFORMATION

Citation

Anne-Katrin Emde et al.
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
Bioinformatics (2012) 28 (5): 619-627.