Home
Conterminator is an efficient method to detect incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison. It is free open-source GPLv3-licensed software for Linux and macOS, and is developed on top of modules provided by MMseqs2.
Conterminator can be installed by compiling from source. It requires a 64-bit system (check with uname -a | grep x86_64) with at least the SSE4.1 instruction set (check by executing cat /proc/cpuinfo | grep sse4_1 on Linux or sysctl -a | grep machdep.cpu.features | grep SSE4.1 on macOS).
git clone --recursive https://github.com/martin-steinegger/conterminator
mkdir conterminator/build && cd conterminator/build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
make -j 4
make install
export PATH=$(pwd)/bin/:$PATH
Conterminator computes ungapped local alignments of all sequence and reports contamination across user-specifed specified taxa, by default this is done at kingdom level.
To process nucleotide sequences use the following command:
conterminator dna example/dna.fas example/dna.mapping result tmp
Conterminator requires a FASTA input and mappingFile file, which maps FASTA identfiers to NCBI taxon identfiers.
Protein sequences can be processed as following:
conterminator protein example/prots.fas example/prots.mapping result tmp
This parameters controls across which ranks contaminations should be considered.
Each taxon definition is seperated by a , e.g. to search for contamination between bacteria and human use --taxon-list 2,9606.
It is also possible to use more advanced expressions for contamination rules, through the following operators:
! NEGATION
|| OR
&& AND
The default rule is as follows:
2||2157,4751,33208,33090,2759&&!4751&&!33208&&!33090
This searches for contamination between the following taxa:
2||2157 # Bacteria OR Archaea
4751 # Fungi
33208 # Metazoa
33090 # Viridiplantae
2759&&!4751&&!33208&&!33090 # Eukaryota without Fungi Metazoa and Viridiplantae