contigtax is a tool that assigns taxonomy to metagenomic contigs by querying contig nucleotide sequences against a protein database using diamond blastx and parses hits using rank-specific thresholds. The use of rank-specific thresholds was first introduced by Luo et al 2014 and used with some modification as explained in Alneberg et al 2018.

Simplest way to install contigtax is via conda:

conda install -c bioconda contigtax

Alternatively, pull the docker image:

docker pull nbisweden/contigtax

1. Download fasta file

contigtax download uniref100

2. Download NCBI taxonomy

contigtax download taxonomy

3. Reformat fasta file and create taxonmap

contigtax format uniref100/uniref100.fasta.gz uniref100/uniref100.reformat.fasta.gz

4. Build diamond database

contigtax build uniref100/uniref100.reformat.fasta.gz uniref100/prot.accession2taxid.gz taxonomy/nodes.dmp

5. Search (here assembled contigs are in file assembly.fa)

contigtax search -p 4 assembly.fa uniref100/diamond.dmnd assembly.tsv.gz

6. Assign (here output from the contigtax search step are in file assembly.tsv.gz)

contigtax assign -p 4 assembly.tsv.gz assembly.taxonomy.tsv

To run contigtax with docker simply substitute contigtax in the commands above with docker run --rm -v $(pwd):/work nbisweden/contigtax, e.g.:

1. Download fasta file

docker run --rm -v $(pwd):/work nbisweden/contigtax download uniref100

2. Download NCBI taxonomy

docker run --rm -v $(pwd):/work nbisweden/contigtax download taxonomy

3. Reformat fasta file and create taxonmap

docker run --rm -v $(pwd):/work nbisweden/contigtax format uniref100/uniref100.fasta.gz uniref100/uniref100.reformat.fasta.gz

4. Build diamond database

docker run --rm -v $(pwd):/work nbisweden/contigtax build uniref100/uniref100.reformat.fasta.gz uniref100/prot.accession2taxid.gz taxonomy/nodes.dmp

5. Search (here assembled contigs are in file assembly.fa)

docker run --rm -v $(pwd):/work nbisweden/contigtax search -p 4 assembly.fa uniref100/diamond.dmnd assembly.tsv.gz

6. Assign (here output from the contigtax search step are in file assembly.tsv.gz)

docker run --rm -v $(pwd):/work nbisweden/contigtax assign -p 4 assembly.tsv.gz assembly.taxonomy.tsv