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.

• NCBI C++ Toolkit
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• NCBI C++ Toolkit documentation
• NCBI C++ Toolkit book

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