Blobtools

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step.

Input files:

1. BLAST results in a tab-separated-values file with very specific data in each column, which you can produce using this command:
   blastn -query assembly_file.fasta -db /mnt/databases/NCBI/nt -outfmt "6 qseqid staxids bitscore std" -max_target_seqs 1 -max_hsps 1 -num_threads 4 -evalue 1e-25 -out results_file.txt

2. A sorted BAM mapping file which you can obtain by converting (and sorting) the SAM generated previously:
   samtools view -Sb mapping.sam > mapping.bam
samtools sort mapping.bam mapping_sorted.bam

To run the first step of blobtools (creating a database file), run this command:
/opt/blobtools/blobtools create -i assembly.fasta -b mapping_sorted.bam -t blastresults.txt -o filename

:exclamation: All the input files have to be in the same folder as in order to run this command.

The next step is creating a table with results:
/opt/blobtools/blobtools view -i filename.blobDB.json

For a visualization of the results and a basic statistic of taxa that the sequences are associated with, use:

/opt/blobtools/blobtools blobplot -i filename.blobDB.json

Now, since blobtools is a tool for detection (and quantification) of contamination in the data, it would be rather convenient to also mention how to remove the contaminating sequences. For example, let’s assume that blobtools associated some of the sequences with Firmicutes and you’re pretty sure that’s not what you’re looking for in the data. To remove these sequences from your assembly, you can use a set of commands:
grep -v "Firmicutes" blobtools_view_output.blobDB.table.txt > blobtools_table_without_firmicutes.txt
cut -f 1,1 blobtools_table_without_firmicutes.txt > node_names.txt
/opt/scripts/fasta_tool --select node_names.txt assembly.fasta > assembly_clean.fasta

What’s left in the assembly_clean.fasta file is your assembly without the Firmicutes-associated sequences. At this point, it might be useful to compare this new assembly file with the old one (e.g. by QUAST) to see what changed after removal of the contaminations - for example, to see if there’s anything left in your assembly.

KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra
KAT

MCSC

pipeline for decontamination of biological sequences

MCSC_DEcontamination