Supported Short Read Aligners

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SHORE currently supports the following alignment tools:

All tools are available as free download for academic use. These tools need 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 alignment tool depends on the type of project as each tool has some pros and cons. The following list is based on our everyday's struggle experiences and might be different to yours:


Pro: Adjustable for high number of mismatches and gaps, long reads, accurate alignments (Needleman-Wunsch like)
Con: Gapped alignments are slower than ungapped alignments.
Recommended for: Genome resequencing, high polymorphism density, most other applications
Version: 0.4.? or higher


Pro: Fast and small memory requirement, unlimited mismatches and gaps.
Con: Currently no spliced alignment support
Recommended for: Any Illumina GA data
Version: 0.5.9 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
Version: 0.12.7 or higher


Pro: It's fast
Con: Only up to two mismatches and no gaps allowed
Recommended for: Rapid testing
Version: CASAVA v1.7.0 or higher


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: 2.07.07 or higher


Pro: Spliced alignments
Con: Slow
Recommended for: Spliced alignment of leftover reads
Version: 2011-03-28 or higher


Pro: Spliced alignment
Con: Slow
Recommended for: Spliced alignment of leftover reads
Version: 34 or higher