RazerS—fast read mapping with sensitivity control
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TLDR
This work presents an efficient read mapping tool called RazerS, which allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance and guarantees not to lose more reads than specified.Abstract:
Second-generation sequencing technologies deliver DNA sequence data at unprecedented high throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. Due to the large amounts of data, efficient algorithms and implementations are crucial for this task. We present an efficient read mapping tool called RazerS. It allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. Our tool can work either lossless or with a user-defined loss rate at higher speeds. Given the loss rate, we present an approach that guarantees not to lose more reads than specified. This enables the user to adapt to the problem at hand and provides a seamless tradeoff between sensitivity and running time. [RazerS is freely available at http://www.seqan.de/projects/razers.html.]read more
Citations
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Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Thomas D. Wu,Serban Nacu +1 more
TL;DR: Computational methods for fast detection of complex variants and splicing in short reads, based on a successively constrained search process of merging and filtering position lists from a genomic index are presented.
Journal ArticleDOI
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Marcel H. Schulz,Marcel H. Schulz,Marcel H. Schulz,Daniel R. Zerbino,Daniel R. Zerbino,Martin Vingron,Ewan Birney +6 more
TL;DR: A software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms is presented.
Journal ArticleDOI
Assembly algorithms for next-generation sequencing data.
TL;DR: This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo to compare the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.
Journal ArticleDOI
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
Mark Chaisson,Glenn Tesler +1 more
TL;DR: The results indicate that it is possible to map SMS reads with high accuracy and speed, and the inferences made on the mapability of SMS reads using the combinatorial model of sequencing error are in agreement with the mapping accuracy demonstrated on simulated reads.
References
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Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
Identification of common molecular subsequences.
TL;DR: This letter extends the heuristic homology algorithm of Needleman & Wunsch (1970) to find a pair of segments, one from each of two long sequences, such that there is no other Pair of segments with greater similarity (homology).
Journal Article
Binary codes capable of correcting deletions, insertions, and reversals
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
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