Difference between revisions of "Smalt"
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| − | [[Category:Software | + | [[Category:Software]][[Category:biology]][[Category:phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|smalt}} | |{{#vardefine:app|smalt}} | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - user manual directory |
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 17:24, 3 June 2022
Description
SMALT aligns DNA sequencing reads with a reference genome.
Supported Sequencing Platforms ============================== Reads from a wide range of sequencing platforms can be processed, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads are supported. There is no support for SOLiD reads.
Strategy ======== The software employs a hash index of short words of up to 20 nucleotides sampled at equidistant steps along the reference genome. For each sequencing read, potentially matching segments in the reference genome are identified from seed matches in the index and subsequently aligned with the read using dynamic programming.
Environment Modules
Run module spider smalt to find out what environment modules are available for this application.
System Variables
- HPC_SMALT_DIR - installation directory
- HPC_SMALT_BIN - executable directory
- HPC_SMALT_DOC - user manual directory