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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

NCBI C++ Toolkit

The NCBI C++ Toolkit is a large collection of libraries and applications from NCBI for working with biological sequence data and the associated ASN.1 data formats. On Roihu it is provided mainly for the command-line utilities it installs.

License

The NCBI C++ Toolkit is released into the public domain by the US National Center for Biotechnology Information. See the NCBI C++ Toolkit documentation for details.

Available

  • Roihu: 28_0_12 (module ncbi-toolkit), via the bio-apps module.

Usage

The NCBI C++ Toolkit is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load ncbi-toolkit/28_0_12

The module installs a large number of programs. Most are the toolkit's own internal test, sample and database-driver programs (for example unit_test_*, test_*, odbc100_*, tds100_*), which are not intended for end users. The user-facing command-line applications include:

  • ASN.1 and data-conversion tools: datatool, asn2asn, asn2fasta, asn2flat, asnvalidate, asn_cleanup, table2asn, tableval, idfetch, srcchk, agpconvert, agp_validate, multireader.
  • Sequence-analysis tools: splign, nw_aligner, vecscreen, windowmasker.
  • The BLAST+ programs (blastn, blastp, makeblastdb, …). For standalone BLAST searches, the dedicated blast-plus module is the recommended option.

For example, to convert an ASN.1 file to FASTA with asn2fasta:

asn2fasta -i input.asn -o output.fasta

Example batch script

#!/bin/bash
#SBATCH --job-name=ncbi-toolkit
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G

module load bio-apps/v202603
module load ncbi-toolkit/28_0_12

table2asn -indir submission_files -outdir asn_out

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information