metagen utils

This consists of 2 tools for analysis of metagenomic DNA from sediments.

• kraken_report is a rewrite in python of the original kraken-report.pl perl script.

  • You can now fetch back reads assigned by kraken, for user-defined clades
  • Improved speed

• chunk_genome provides functions used to generate reads derived from a set of sequences (i.e. full genome FASTA file).

  • You can specify a mutation rate, a VCF file in order to add known SNPs, or a mutation matrix obtained from snpAD

  Kay Prüfer, snpAD: an ancient DNA genotype caller, Bioinformatics, Volume 34, Issue 24, 15 December 2018, Pages 4165–4171, https://doi.org/10.1093/bioinformatics/bty507.

  • Default read length distribution is uniform, but you can provide your own (see Data).
  • Work is processed in parallel in order to decrease computation time.

Usage

Examples

• Report the clade assignment from the output of kraken and extract the sequences for clade 9606

  python3 -m metagen_utils.kraken_report --db ${KRAKEN_DB_PATH} --clades 90606 --outdir results \

  --extractFile sourcefile.fa sourcefile.fa.kraken

• Generate 30 reads with a specific deamination pattern only using the 1st chromosome of the source_genome

  python3 metagen_utils.chunk_genome --subst ${DATA}/substitution_matrix.tsv --num_seq 30 \

  --chrom 1 --outfile simulated_reads.fa source_genome.fa

Installation

pip install --user metagen_utils-VERSION.tar.gz

python -m metagen_utils.chunk_genome -h

- or -

unpack

cd /WHERE_UNPACKED

python -m metagen_utils-VERSION.chunk_genome -h

Data

Files present in data/ are are empirical values which enable chunk_genome to create simulated reads close to what one would expect in reality regarding degradation of DNA and read length distribution. Copy them for further use as they wont be installed automatically.

kraken_report needs trimmed data from the NCBI taxonomy ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz put in you kraken taxonomy folder

On UNIX:

grep 'scientific name' names.dmp |cut -d'|' -f 1,2 |gzip -c > ${KRAKEN_DB_PATH}/taxonomy/names_trimmed.dmp.gz

cut -d '|' -f 1,2,3 nodes.dmp|gzip -c > ${KRAKEN_DB_PATH}/taxonomy/nodes_trimmed.dmp.gz

generate the doc using SPHINX

unpack

cd metagen_utils-VERSION

python setup.py build_sphinx