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.
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:
- identification of candidate regions from the genome to be assessed with tBLASTn searches using BUSCO consensus sequences.
- Gene structure prediction using Augustus with BUSCO block profiles.
- 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".
After the first blastn, augustus is invoked as follows:
augustus --proteinprofile=example/prfl/BUSCO_7.prfl --predictionStart=163394 --predictionEnd=174110 --species=fly "sampleasroo2_.temp" > ./run_asroo2//augustus/BUSCO_7.out.1 2>/dev/null
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
However, there is a symlink to this called BUSCO, so the program can equally well be launched with a simple
BUSCO has the following three modes
- Genome assembly assessment, i.e. -m genome
- Transcriptome assembly assessment i.e. -m trans
- Gene set assessment i.e. -m ogs
typical usage command lines
After loading the module, the template is as follows:
BUSCO -o NAME -in ASSEMBLY -l LINEAGE -m genome
- -o is simply for giving a name to an output directory where various output files will be stored. run_' will be put in front of this name.
- -in is you data input, which for BUSCO is the assembled genome.
- -l is the lineage, which can be one of the following: $METAZOA_LIN, $EUKARYOTA_LIN, $BACTERIA_LIN, $ARTHROPODA_LIN, $VERTEBRATA_LIN, $FUNGI_LIN: these are variables telling BUSCO where to look.
- -m as already explained this is the mode.
So, a typical command on a bacteria assembly would run like this:
BUSCO -in scaffolds.fasta -o busc0 -l $BACTERIA_LIN -m genome
There is a certain error, which, because it only refers to the retaining operation, can be safely ignored (unless when wanting to retrain of course)
Error: Cannot write to Augustus directory, please make sure you have write permissions to /usr/local/Modules/modulefiles/tools/augustus/3.2.2/config