Using Blobtools to remove sequence contamination

Question

[kristina.mahan]

I would like to use blobtools to filter out contaminating sequences from by genome assemblies. Inputs are assembly fasta, coverage file (bam), and a hits file. How do we make the hits file from a BLAST database?

Answer 1

[h.mon]

See the documentation here: Hits file. For example, using blast:

blastn \
    -query $ASSEMBLY \
    -db nt \
    -outfmt ’6 qseqid staxids bitscore std’ \
    -max_target_seqs 10 \
    -max_hsps 1 \
    -evalue 1e-25