Tutorial

Welcome to the BinBlaster wiki!

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usage: BinBlast.py [-h] [-fasta FASTA] [-ref REF] [-bam BAM] [-out OUT] [-t T]

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Developed by Arkadiy Garber; University of Montana, Biological Sciences Please send comments and inquiries to [email protected]

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optional arguments:

-h, --help show this help message and exit

-g [file] Input bin/assembly in FASTA format

-o [file] Input ORFs from bin/assembly in FASTA amino acid format

-ref [file] Input reference protein database (recommended: nr)

-bam [file] Input sorted BAM file with coverage info (optional)

-out [file] Name output file

-t [int] Number of threads to use for DIAMOND BLAST

Sample command if providing contigs belonging to a metagenome bin:

./BinBlast -g mybin1.fasta -ref /path/to/nr.faa -bam assemblyCovereage.sorted.bam -out mybin1.summary.csv -t 4

Sample command if providing open reading frames belonging to a metagenome bin:

./BinBlast -o mybin1-ORFs.faa -ref /path/to/nr.faa -bam assemblyCovereage.sorted.bam -out mybin1.summary.csv -t 4