Fast and accurate mapping of complete genomics reads
Date
2015Source Title
Methods
Print ISSN
1046-2023
Publisher
Academic Press
Volume
79-80
Pages
3 - 10
Language
English
Type
ArticleItem Usage Stats
154
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views
119
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downloads
Abstract
Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of different sequencing technologies currently available, and each HTS platform have different strengths and biases. This diversity both makes it possible to use different technologies to correct for shortcomings; but also requires to develop different algorithms for each platform due to the differences in data types and error models. The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available and open source aligners are still lacking for the Complete Genomics (CG) platform. Unfortunately, Burrows-Wheeler based methods are not practical for CG data due to the gapped nature of the reads generated by this method. Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. We evaluate the performance and accuracy of sirFAST using both simulated and publicly available real data sets, showing high precision and recall rates.
Keywords
Complete genomicsGapped reads
High throughput sequencing
Read mapping
DNA
Accuracy
Controlled study
Data analysis software
DNA sequence
Gene mapping
Genetic algorithm
Genomics
High throughput sequencing
Human
Human genome
Indel mutation
Personalized medicine
Priority journal
Sensitivity and specificity