Light version of the upcoming blobtools package
blobtools-light allows the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots (Kumar et al. 2012).
Software requirements:
Data requirements:
Making blobplot file:
usage: makeblobs.py -a <ASSEMBLY> -cas <CAS> -blast <BLAST> -taxdb <PATH_TO_TAXDB> -o <OUTPUT> [-h]
optional arguments:
-h, --help show this help message and exit
-a ASSEMBLY_FASTA Assembly file
-spades SPADES_FASTA SPADES assembly file
-velvet VELVET_FASTA VELVET assembly file
-abyss ABYSS_FASTA ABYSS assembly file
-exclude_assembly_cov Exclude coverage from assembly file
-cov COV_FILE [COV_FILE ...] COV (mapping) file(s)
-bam BAM_FILE [BAM_FILE ...] BAM (mapping) file(s)
-sam SAM_FILE [SAM_FILE ...] SAM (mapping) file(s)
-cas CAS_FILE [CAS_FILE ...] CAS (mapping) file(s)
-blast BLAST_FILE [BLAST_FILE ...] BLAST file(s)
-rank TAX_RANK Select target taxonomic rank (species, genus, order,
phylum, superkingdom). Default = phylum
-taxrule A or B Tax-rule on how to deal with multiple BLAST libs. A :
"higher bitscore wins", B : "Decreasing trust in BLAST
libs"
-taxdb TAX_DUMP Path to NCBI taxdb (nodes.dmp, names.dmp)
-o OUTPUT_PREFIX Output prefix
-v show program's version number and exit
>> ~/blobtools-light/makeblobs.py -a assembly/assembly.fa -bam mapping/assembly.mapping.bam -taxdb /exports/blast_db/ -blast assembly.vs.nt.25cul1.1e25.megablast.out -o test
Plotting blobplot-file:
~/blobtools-light/plotblobs.py test.blobplot.txt