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DIAMOND BLASTP is DIAMOND's mode for protein sequence searches. For more information, see the tool's GitHub repo and wiki.

Function Call


Function Arguments

See the Notes section below for more details.

Argument Use in place of: Description
inputs -q, --query Path to one or more files to use as input. FASTA or FASTQ formats are supported, as well as gzip-compressed FASTA/FASTQ files. The files can be a local or remote, see Using Files.
output_path -o, --out (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Using Files.
database_name -d (optional) Name of database to use for DIAMOND BLASTP. Defaults to "diamond_blastp_standard", the SeqScreen database.
database_version database version (optional) Version of database to use for DIAMOND BLASTP. Defaults to "1".
remote_database_path -d (path) (optional) AWS S3 URI to the directory that contains your custom database.
remote_database_primary_name -d (name) (optional) The primary name (e.g. of your custom database.
tool_args all other arguments (optional) Additional arguments to be passed to Diamond BLASTp. This should be a string of arguments like the command line.
is_async Whether to run a job asynchronously. See Async Runs for more.

DIAMOND BLASTP runs are aligned against the SeqScreen database by default. See the Databases section for more details.

Tool Versions

Toolchest currently supports version 2.0.14 of DIAMOND.


Toolchest currently supports the following databases for DIAMOND BLASTP:

database_name database_version Description
diamond_blastp_standard 1 SeqScreen DIAMOND BLASTP Database. See the SeqScreen wiki for more details.

Supported Additional Arguments

  • -f
  • --fast
  • -l
  • --mid-sensitive
  • --min-orf
  • --more-sensitive
  • --no-self-hits
  • --outfmt
  • --sallseqid
  • --salltitles
  • --sensitive
  • --strand
  • --ultra-sensitive
  • --unal
  • --very-sensitive

Additional arguments can be specified under the tool_args argument.