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Tools installed in the container image

This page documents all third-party tools bundled in the skimindex container image. Versions are pinned in docker/Makefile and substituted at build time via --build-arg.

OBITools4

Bioinformatics suite for the analysis of DNA metabarcoding data. Provides sequence manipulation, demultiplexing, taxonomic assignment, and quality filtering.
Version 4.4.29 (pinned; OBITOOLS_VERSION in docker/Makefile)
Binary location /usr/local/bin/obi*
Architecture Compiled from source for each target platform (builder stage)
Language Go
GitHub https://github.com/metabarcoding/obitools4
Documentation https://obitools4.metabarcoding.org/
Institution LECA / Université Grenoble Alpes

Reference

Boyer F., Mercier C., Bonin A., Le Bras Y., Taberlet P., Coissac E. (2016). obitools: a unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources, 16(1), 176–182. https://doi.org/10.1111/1755-0998.12428

kmindex

Fast and memory-efficient k-mer indexing and querying across large collections of genomic datasets. Used by skimindex for decontamination k-mer index construction and querying.
Version latest bioconda release (bioconda::kmindex)
Binary location /opt/conda/bin/kmindex
Architecture linux/amd64, linux/arm64
Language C++
GitHub https://github.com/tlemane/kmindex
Documentation https://tlemane.github.io/kmindex

References

Lemane T., Lezzoche N., Lecubin J., Pelletier E., Sunagawa S., Bork P., Hingamp P., Lavigne R., Chikhi R., Peterlongo P. (2024). Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA. Nature Computational Science, 4, 104–109. https://doi.org/10.1038/s43588-024-00596-6

Lemane T., Medvedev P., Chikhi R., Peterlongo P. (2022). kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections. Bioinformatics Advances, 2(1), vbac029. https://doi.org/10.1093/bioadv/vbac029

ntCard

Streaming algorithm for estimating k-mer frequency histograms from sequencing data. Used to estimate genome size and coverage prior to k-mer counting.
Version latest bioconda release (bioconda::ntcard)
Binary location /opt/conda/bin/ntcard
Architecture linux/amd64, linux/arm64
Language C++
GitHub https://github.com/bcgsc/ntCard
Website https://bcgsc.ca/resources/software/ntcard

Reference

Mohamadi H., Khan H., Birol I. (2017). ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinformatics, 33(9), 1324–1330. https://doi.org/10.1093/bioinformatics/btw832

NCBI SRA Toolkit

Suite of tools for downloading, validating, and converting sequencing data from the NCBI Sequence Read Archive (SRA). Provides prefetch, fasterq-dump, sam-dump, and many others.
Version 3.2.0 (latest bioconda; bioconda::sra-tools)
Binary location /opt/conda/bin/prefetch, /opt/conda/bin/fasterq-dump, …
Architecture linux/amd64, linux/arm64 (via bioconda + conda-forge::ossuuid)
Language C / C++
GitHub https://github.com/ncbi/sra-tools
Documentation https://github.com/ncbi/sra-tools/wiki
Website https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/
Institution NCBI / National Library of Medicine

Reference

Leinonen R., Sugawara H., Shumway M., International Nucleotide Sequence Database Collaboration (2011). The sequence read archive. Nucleic Acids Research, 39(Database issue), D19–D21. https://doi.org/10.1093/nar/gkq1019

NCBI Datasets CLI

Command-line interface for downloading genome assemblies, gene sequences, and associated metadata directly from NCBI. Provides datasets and dataformat.
Version v18.21.0 (pinned; NCBI_DATASETS_VERSION in docker/Makefile)
Binaries /usr/local/bin/datasets, /usr/local/bin/dataformat
Architecture linux/amd64, linux/arm64 (official NCBI releases)
Language Go
GitHub https://github.com/ncbi/datasets
Documentation https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/
Institution NCBI / National Library of Medicine

IBM Aspera Transfer SDK (ascp)

High-speed file transfer client using the FASP protocol. Used by the SRA Toolkit to accelerate downloads from NCBI when available, falling back transparently to HTTPS otherwise.
Version 1.1.7 (pinned; ASPERA_SDK_VERSION in docker/Makefile)
Binary /usr/local/bin/ascp
Architecture linux/amd64 (linux-amd64), linux/arm64 (linux-aarch64)
Distribution IBM CloudFront CDN (d3pgwzphl5a0ty.cloudfront.net)
Documentation https://www.ibm.com/docs/en/ahts/4.4.x
SDK https://developer.ibm.com/apis/catalog/aspera--aspera-transfer-sdk/
Website https://www.ibm.com/products/aspera
Institution IBM
SRA integration Configured via vdb-config --set /TOOLS/ascp-path=/usr/local/bin/ascp

Note: ARM64 support was introduced in SDK 1.1.4 (transferd 1.1.4).

kmerasm

Simple de Bruijn unitig assembler for 31-mers. Reads canonical 31-mers (one per line) and outputs unitigs in FASTA format, built from non-branching paths in the de Bruijn graph.
Version in-house (built from src/kmerasm/)
Binary /app/bin/kmerasm
Architecture Compiled for each target platform (builder stage)
Language C
Source src/kmerasm/kmerasm.c in this repository

Base environment

Miniconda3 / conda
Base image continuumio/miniconda3:latest
Python /opt/conda/bin/python3
Website https://docs.conda.io

Tools installed via conda are in /opt/conda/bin/ and available on PATH.

System utilities (apt)

Installed via apt-get in the container:

Tool Purpose
pigz Parallel gzip compression / decompression
jq JSON processor
curl HTTP/FTP client
make Build automation
less Pager
sudo Privilege escalation (user skimindex has NOPASSWD:ALL)

Version management

All pinned versions are centralised in docker/Makefile:

OBITOOLS_VERSION      := 4.4.29
NCBI_DATASETS_VERSION := v18.21.0
KMINDEX_VERSION       := bioconda::kmindex
NTCARD_VERSION        := bioconda::ntcard
SRATOOLS_VERSION      := bioconda::sra-tools
ASPERA_SDK_VERSION    := 1.1.7

To update a tool, change the corresponding variable and rebuild with make all.