Difference between revisions of "Last"

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m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ")
 
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__NOTOC__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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[[Category:Software]][[Category:Biology]][[Category:Alignment]][[Category:Sequencing]]
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{|<!--Main settings - REQUIRED-->
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Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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{|
 
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|{{#vardefine:app|last}}
 
|{{#vardefine:app|last}}
 
|{{#vardefine:url|http://last.cbrc.jp/}}
 
|{{#vardefine:url|http://last.cbrc.jp/}}
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
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LAST cannot (yet):
 
LAST cannot (yet):
 
* Do spliced alignment
 
* Do spliced alignment
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==Environment Modules==
==Available versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 193 (EL5)
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#if: {{#var: testing}}|==Performance==

Latest revision as of 19:29, 12 August 2022

Description

last website  

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

Environment Modules

Run module spider last to find out what environment modules are available for this application.

System Variables

  • HPC_LAST_DIR - installation directory