Konnector v2.0: pseudo-long reads from paired-end sequencing data.

ABSTRACT:

Background

Reading the nucleotides from two ends of a DNA fragment is called paired-end tag (PET) sequencing. When the fragment length is longer than the combined read length, there remains a gap of unsequenced nucleotides between read pairs. If the target in such experiments is sequenced at a level to provide redundant coverage, it may be possible to bridge these gaps using bioinformatics methods. Konnector is a local de novo assembly tool that addresses this problem. Here we report on version 2.0 of our tool.

Results

Konnector uses a probabilistic and memory-efficient data structure called Bloom filter to represent a k-mer spectrum - all possible sequences of length k in an input file, such as the collection of reads in a PET sequencing experiment. It performs look-ups to

SUBMITTER: Vandervalk BP 

PROVIDER: S-EPMC4582294 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature