Using Blobtools to remove sequence contamination
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10 months ago

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?

bast database blobtools • 591 views
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Entering edit mode
10 months ago
h.mon 32k

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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