A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
FANGS: high speed sequence mapping for next generation sequencers
Proceedings of the 2010 ACM Symposium on Applied Computing
MPSCAN: fast localisation of multiple reads in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
REAL: an efficient REad ALigner for next generation sequencing reads
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Design of an efficient out-of-core read alignment algorithm
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Journal of Parallel and Distributed Computing
Metamorphic slice: An application in spectrum-based fault localization
Information and Software Technology
SEME: a fast mapper of illumina sequencing reads with statistical evaluation
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
Frequency-based re-sequencing tool for short reads on graphics processing units
International Journal of Computational Science and Engineering
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Summary: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions/deletions of the nucleotide bases in the sequences can be tolerated and therefore detected. SeqMap supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process. A typical mapping can be done in a few hours on a desktop PC. Parallel use of SeqMap on a cluster is also very straightforward. Contact: whwong@stanford.edu