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

TL;DR

SlopMap is a software tool designed for quick, flexible identification of similar sequences using exact k-mer matching, facilitating integration into bioinformatics pipelines for targeted sequence extraction from NGS data.

Contribution

It introduces SlopMap, a novel utility that enables rapid sequence similarity identification with exact k-mer matching, compatible with existing assembly workflows and preserving flowgram data.

Findings

Supports Roche 454 and Illumina data

Provides compatible output formats for assembly

Enables pipeline integration without extra programming

Abstract

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome 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 in- compatibility with the assembler's file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is necessary to first extract them from the original SFF files. We present SlopMap, a bioinformatics software utility which allows rapid identification similar to provided target sequences from either Roche 454 or Illumnia DNA library. With a simple and intuitive command- line interface along with file output formats compatible with assembly programs, SlopMap can be directly embedded in biological data processing pipeline without any additional programming work. In addition, SlopMap preserves flowgram information needed for Roche 454 assembler.