Supported Short Read Aligners

In addition to GenomeMapper, SHORE supports Eland (included in GA Pipeline), BWA (http://bio-bwa.sourceforge.net/), Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) and Novocraft (http://www.novocraft.com). All tools are available as free download for academic use. These tools have to be installed according to their manuals. Note that we do not guarantee that future developments will be available for all of these tools. The selection of the mapping tool depends on the type of project as each tool has some pros and cons. This list is based on our everyday’s struggle experiences and might be different to yours:

GenomeMapper

Pro: Adjustable for high number of mismatches and gaps, long reads, accurate align- ments (Needleman-Wunsch like) Con: Gapped alignments are slower than ungapped alignments. Recommended for: genome re-sequencing, high polymorphism density, spliced align- ments and any other applications Version: 0.4.2 or higher BWA: Pro: Fast and small memory requirement, unlimited mismatches and gaps.

Con: Currently no spliced alignment or BS-seq support Recommended for: any Illumina GA or SOLiD data (except see above)

Bowtie

(Version: 0.5.7 or higher)

Pro: Small index size due to Burrows-Wheeler compression

Con: Only up to three mismatches and no gaps allowed Recommended for: large genomes and low polymorphism density, servers with small memory

Eland

(Version: 0.12.3 or higher)

Pro: Its fast.

Con: Only up to two mismatches and no gaps allowed Recommended for: rapid testing

Novocraft

(Version: Illumina GA Pipeline 1.3 or 1.4)

Pro: Unlimited number of mismatches and gaps.

Con: Seems to be slow, especially for long reads and high number of mismatches/gaps. Recommended for: currently not recommended due to insufficient testing of the SHORE wrapper for novo Version: 2.05.31 or higher