4. Process BLAST results to remove contamination

After de novo transcriptome assembly, BLASTN can be used to detect contaminated transcripts that should be removed from the assembly.

4.1. Elastic-Blast

Run elastic-blast in your cloud provider as explined here.

Use as options in the ini file:

options = -task megablast -evalue 0.0001 -outfmt "6 qseqid sgi saccver length pident evalue bitscore score qcovs qcovhsp qcovus staxid"

After processing, elastic-blast will create multiple files with extension .out.gz

Download those file to a local folder.

4.2. Remove contamination

Install GTax as described in the Installation.

Run this command to detect and remove contaminated transcripts.

localhost:~> taxonomy_blast --threads 8 --prefix Trinity --fasta Trinity.fasta.gz --taxid 33090 --blastdir ./ --blast_columns "qseqid sgi saccver length pident evalue bitscore score qcovs qcovhsp qcovus staxid"

–taxid option refers to the parent taxonomy ID to use as valid taxonomies. For instance, to process plant transcriptome, use taxid as 33090 which is the taxid of the Viridiplantae kingdom.

Two files will be created using the –prefix option, in this case Trinity:

• Trinity_clean.fsa: FASTA file with decontaminated transcriptome

• Trinity_cont.tsv: TSV file with transcript’s ID and best contaminated BLAST hit