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Using Blobtools to remove sequence contamination

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?

blobtools
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updated by Ram Ram • written by kristina.mahan kristina.mahan

1 answer

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
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written by h.mon h.mon

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