Difference between revisions of "Last"
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Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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__NOEDITSECTION__ | __NOEDITSECTION__ | ||
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | ||
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|last}} | |{{#vardefine:app|last}} | ||
|{{#vardefine:url|http://last.cbrc.jp/}} | |{{#vardefine:url|http://last.cbrc.jp/}} | ||
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| − | |||
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
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WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:22, 6 December 2019
Description
LAST finds similar regions between sequences.
What distinguishes LAST from BLAST and similar tools (e.g. BLAT, LASTZ, YASS)? The main difference is that it copes more efficiently with repeat-rich sequences (e.g. genomes). For example, it can align reads to genomes without repeat-masking and without becoming overwhelmed by repetitive hits.
LAST can:
- Handle big sequence data, e.g:
- Compare two vertebrate genomes
- Align billions of DNA reads to a genome
- Indicate the reliability of each aligned column.
- Use sequence quality data properly.
- Compare DNA to proteins, with frameshifts.
- Compare PSSMs to sequences
- Calculate the likelihood of chance similarities between random sequences.
LAST cannot (yet):
- Do spliced alignment
Required Modules
Serial
- last
System Variables
- HPC_LAST_DIR - installation directory
Validation
- Validated 4/5/2018