Difference between revisions of "BUSCO"

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BUSCO is primarily a python application and though it can, apparently, work with version 2 of python, version 3 is recommended.
 
BUSCO is primarily a python application and though it can, apparently, work with version 2 of python, version 3 is recommended.
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The broad BUSCO process is as follows:
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# identification of candidate regions from the genome to be assessed  with  tBLASTn  searches  using  BUSCO  consensus  sequences.
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# Gene  structure prediction using Augustus with BUSCO block profiles.
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# These predicted genes, or all genes from an annotated gene set or transcriptome, are assessed using HMMER and lineage-­
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specific  BUSCO  profiles  to  classify  matches  as  "complete", "duplicated", or "fragmented", or when there are no matches, as "missing".
  
 
= Using =
 
= Using =

Revision as of 10:31, 27 July 2016

Introduction

BUSCO, like Cegma, is a special tool for the field of "completeness assessment". This concerns genome assemblies, particularly ones generated de-novo, when by concentrating on a core set of genes, one can estimate how complete the assembly is by the number of the these core geens that the assembly has managed to recover.

BUSCO actually stands for "Benchmarking Universal Single-­Copy Orthologs" and labels itself as a quality measure of the assembly. Busco also means "I search" in the Spanish, Galician and Portuguese languages, in which the authors find satisfaction, as the broad goal of the tool is one of a quest for quality.

Aspects

BUSCO can work closely with augustus, even as far as undertaking retraining (for a species). However, take note:

"Write access to the Augustus installation directory is necessary for retraining the gene finder", so retraining is probably best carried out by the sysadmin under "root" user.

BUSCO is primarily a python application and though it can, apparently, work with version 2 of python, version 3 is recommended.

The broad BUSCO process is as follows:

  1. identification of candidate regions from the genome to be assessed with tBLASTn searches using BUSCO consensus sequences.
  2. Gene structure prediction using Augustus with BUSCO block profiles.
  3. These predicted genes, or all genes from an annotated gene set or transcriptome, are assessed using HMMER and lineage-­

specific BUSCO profiles to classify matches as "complete", "duplicated", or "fragmented", or when there are no matches, as "missing".

Using

loading the module

module load BUSCO

is enough, as all BUSCO's dependencies (python/3.4, augustus/3.2.2, hmmer/3.1b2, EMBOSS/6.6.0) will also be loaded at the same time.

The main BUSCO executable is a python script called

BUSCO_v1.22.py

However, there is a symlink to this called BUSCO, so the program can equally well be launched with a simple

BUSCO