BUSCO v3 Installation & Usage
BUSCO v3 is a tool providing quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.
BUSCO also provides user guide : BUSCO_v3_userguide.pdf
cite : https://busco.ezlab.org
Installation
I executed BUSCO v3 on Ubuntu Server 16.04 LTS. (Amazon AWS)
- git clone https://gitlab.com/ezlab/busco.git
- move directory to busco.
- sudo python setup.py install.
Installation of BUSCO only is finished.
But, it needs additional software to use BUSCO v3 :( (not described in detail in user guide)
Those are NCBI BLAST+ , HMMER , Augustus.
Especially, installation of Augustus is complex. here is a list of dependency to Augustus.
bamtools, samtools, bcftools, htslib , boost, zlib1g
And, each tool also have a dependency.
bamtools - zlib
htslib - zlib, liblzma, libbzip2
samtools - libncurses5-dev libncursesw5-dev
After installing all dependency to Augustus, should change path of software.
Augustus/auxprogs/bam2hints/Makefile
Augustus/auxprogs/filterBam/src/Makefile
Augustus/auxprogs/bam2wig/Makefile
Then, you can run Augustus perfectly.
I'll post easy-to-use install script soon.
Input
Organism Image Macaca nemestrina (pig-tailed macaque) Macaca nemestrina overview
Usage
python BUSCO.py -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] -sp [SPECIES] (-c [CPU count])
-i FASTA FILE, --in FASTA FILE
-l LINEAGE, --lineage_path Specify location of the BUSCO lineage data to be used.
-o OUTPUT, --out OUTPUT
-m MODE, --mode MODE Specify which BUSCO analysis mode to run.
There are three valid modes:
- geno or genome, for genome assemblies
- tran or transcriptome, for transcriptome assemblies
- prot or proteins, for annotated gene sets (protein)
-sp SPECIES, --species SPECIES
Name of existing Augustus species gene finding
parameters. See Augustus documentation for available
options.
-c N, --cpu N Specify the number (N=integer) of threads/cores to use.
Result
short_summary_result of BUSCO execution
# BUSCO version is: 3.1.0
# The lineage dataset is: mammalia_odb9 (Creation date: 2016-02-13, number of species: 50, number of BUSCOs: 4104)
# To reproduce this run: python busco-master/scripts/run_BUSCO.py -i
data/GCF_000956065.1_Mnem_1.0_genomic.fna -o result -l mammalia_odb9/
-m genome -c 16 -sp human
# Summarized benchmarking in BUSCO notation for file data/GCF_000956065.1_Mnem_1.0_genomic.fna
# BUSCO was run in mode: genome
C:94.7%[S:93.7%,D:1.0%],F:2.1%,M:3.2%,n:4104
3889 Complete BUSCOs (C)
3847 Complete and single-copy BUSCOs (S)
42 Complete and duplicated BUSCOs (D)
88 Fragmented BUSCOs (F)
127 Missing BUSCOs (M)
4104 Total BUSCO groups searched
full_table_result of BUSCO execution
# Busco id Status Contig Start End Score Length
EOG090A0FFC Complete NW_012014355.1 10381323 10382532 144.0 83
EOG090A0FG2 Complete NW_012011723.1 598963 642561 190.4 92
EOG090A0FM8 Complete NW_012012355.1 18069359 18078634 177.3 84
EOG090A0FQ0 Complete NW_012011278.1 5427743 5447851 159.0 77
EOG090A0FRR Complete NW_012012000.1 1219700 1231323 223.9 104
EOG090A0FSN Complete NW_012010800.1 1324877 1365806 212.0 99
EOG090A0FSO Duplicated NW_012014022.1 22365084 22381425 168.5 89
EOG090A0FSO Duplicated NW_012018132.1 13035685 13051851 146.6 88
EOG090A0FTC Complete NW_012011100.1 1044303 1045003 187.3 80
EOG090A0FUE Complete NW_012012244.1 17031932 17032222 147.5 78
EOG090A0FUU Missing
EOG090A0FUY Complete NW_012010745.1 1404622 1453453 475.2 296
EOG090A0FVS Complete NW_012017243.1 22347808 22367367 147.7 75
EOG090A0FW2 Complete NW_012018354.1 12533257 12538646 170.3 96
EOG090A0FXI Complete NW_012013244.1 14331782 14338455 221.1 104
EOG090A0FY5 Complete NW_012012799.1 6543474 6553096 160.1 101
EOG090A0GAQ Complete NW_012010800.1 36211955 36232182 331.4 251