SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching.

ABSTRACT: With the advent of Next-Generation (NG) sequencing, it has become possible to sequence a entire genomes quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorporate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to incompatibility with the assembler's file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order t

SUBMITTER: Zhbannikov IY 

PROVIDER: S-EPMC3882202 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature