PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

Motivation: The explosion of next-generation sequencing data has spawned the design of new algorithms and software tools to provide efficient mapping for different read lengths and sequencing technologies. In particular, ABI's sequencer (SOLiD system) poses a big computational challenge with its capacity to produce very large amounts of data, and its unique strategy of encoding sequence data into color signals

RseqFlow: workflows for RNA-Seq data analysis

NIH/NIMH [5 RC2 MH090047-01]; Transcriptional Atlas of Human Brain Development (TAHBD); Center of Excellence of Genome Sciences: Genomic Analysis of the Genotype-Phenotype Map (NIH/HG) [2 P50 HG002790-06]We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps. Availability and implementation: http://genomics.isi.edu/rnaseq Contact: [email protected]; <[email protected]; [email protected]; [email protected] Supplementary information: http://bioinformatics.oxfordjournals.org/cgi/content/full/btr441/DC1 are available at Bioinformatics online