SHORE Documentation
Contents
Introduction
SHORE is a mapping and analysis pipeline for short DNA sequences produced on Illumina Genome Analyzer and Hiseq 2000, Life Technology SOLiD, 454 Genome Sequencer FLX and PacBio RS platforms. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions.
SHORE provides various prediction algorithms for genomic polymorphisms, i.e. SNPs, structural variants (indels, CNVs, unsequenced regions), SNPs and SV prediction in heterozygous or pooled samples, as well as peak detection for ChIP-Seq analysis and quantitative analysis of mRNA-Seq and sRNA-Seq.
SHORE stores read data, alignments and result files in a predefined folder structure, which makes it possible to keep track of all intermediate steps and, if desired, repeat parts of the analysis. The predefined folder structure has advantages and disadvantages. While there is no freedom in data structuring when applying SHORE, it makes handling of large projects comprising multiple flowcells more convenient. It is in the nature of such projects that it can take weeks to gather all information, while the initial alignments have to be performed as soon as the first flowcell is finished. This requires an extendable mapping and analysis approach keeping all information in a transparent structure. Of course, also smaller projects can benefit from such a data partitioning.
SHORE was designed to run on a multi-core server (32 or 64 bit) with Linux, MacOS (10.5+) or other POSIX compliant operating systems. Required memory depends both on the application and the reference sequence. Medium sized genomes (e.g. D. melanogaster, A. thaliana) can be analyzed with 2-8GB RAM, large genomes (e.g. H. sapiens) with 8-24GB RAM. SHORE is designed to take advantage of multi-core architectures. SHORE incorporates several alignment tools (e.g. GenomeMapper, bwa, bowtie, ELAND) each coming with their own hardware requirements.
Getting help
Mailinglists, Papers, etc.
FAQ
TBD
Getting started
Before using SHORE
Using SHORE
- Running SHORE for the first time - A Quick Guide
- SHORE Overview
- SHORE file formats
- SHORE Subprograms
SHORE Development
How to Cite SHORE
Project Logo
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