S3_decontamination.md

Decontamination

Find hits

BLAST

blastn -query assembly.fasta -db nt -outfmt "6 qseqid staxids bitscore std sscinames scomnames" -max_hsps 1 -evalue 1e-25 -out blast.out

Find BUSCO orthologs

BUSCO

busco --in assembly.fasta --mode genome --out busco_out -l metazoa_odb10

Mapping long reads to the assembly

minimap2

minimap2 -ax map-hifi assembly.fasta hifi_reads.fastq.gz | samtools sort -o minimap2_hifi.bam
minimap2 -ax map-ont assembly.fasta ont_reads.fastq.gz | samtools sort -o minimap2_ont.bam

Create Blobtools directory

Get new_taxdump.tar.gz here

Blobtools2

blobtools add --fasta assembly.fasta --cov minimap2_hifi.bam --hits blast.out --busco busco_out/run_metazoa_odb10/full_table.tsv --taxdump taxdump --create blobdir
blobtools view --local blobdir