blobtools-light

No longer maintained ... please check out blobtools

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:

• Python 2.7+
• Numpy 1.9.1 ('pip install numpy')
• matplotlib 1.4 ('pip install matplotlib')
• NCBI Taxdump (' wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz ')

Data requirements:

• Assembly* (FASTA)
• if assembly was generated through Spades, Abyss or Velvet, coverage can be parsed from contig headers (use e.g. -spades SPADESASSEMBLY); if coverage from assembly is not needed -exclude_assembly_cov can be specified
• Coverage information (one or more):
  • COV (Tab-separated: "header\tcoverage")
  • BAM/SAM**
  • CAS format (CLC mapper) The first time BAM/SAM/CAS file(s) gets parsed, the program will create a COV file for each. If omeanalsysis
• BLAST result (using BLAST 2.2.29+):
  • suggested command : "blastn -task megablast -query ASSEMBLY.fa -db /blast_db/nt -outfmt '6 qseqid staxids bitscore std sscinames sskingdoms stitle' -max_target_seqs 25 -culling_limit 2 -num_threads 16 -evalue 1e-25 -out ASSEMBLY.vs.nt.25cul1.1e25.megablast.out"
  • The important part is "-outfmt '6 qseqid staxids bitscore'"

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