Proksee

Proksee is a suite of command line tools for performing assembly and evaluation of microbial genomes.

Release

v1.0.0a6

• Modifies the Mash database download procedure to write less output.
• Correctly instructs QUAST to use the user-specified minimum contig size.
• Better handling of Mash for species estimation of large assemblies with many contigs.
• Mash may now be run using parallelization.
• Removed possible security vulnerabilities when running subprocesses.
• Better user input checking.

Installation

Proksee requires the following packages:

• Python 3.7
• Pip
• fastp
• Skesa
• Mash
• Quast
• Scipy
• Spades
• wget

This can be accomplished by installing dependencies into a conda environment, using the provided installation script as follows:

conda env create -f environment.yml
conda activate proksee

Proksee can then be installed by running the setup script (when inside the Proksee directory):

pip install .

Finally, download and install the Mash sketch database required by Proksee by running:

proksee updatedb

Assemble

The assemble pipeline consists of three major stages:

• Stage 1: Pre-Assembly: Verifies inputs, estimates information about the reads, filters the reads, and prepares the reads for sequence assembly.
• Stage 2: Fast Assembly: Assembles the reads quickly in order to derive approximate information about the assembly, such as quality metrics. This information will assist the expert assembly.
• Stage 3: Expert Assembly: Assembles the reads in an expert manner using information gathered during the previous stages.

Please see the documentation for more information about the assemble command.

Command

proksee assemble -o output/directory FORWARD REVERSE

Where the argument provided after -o lets a user to specify a desired output directory. FORWARD and REVERSE are fastq sequencing read files. If REVERSE is not specified, only single strand (FORWARD) is processed by the Proksee pipeline.

Example

proksee assemble -o output forward_reads.fastq reverse_reads.fastq

Evaluate

The evaluate pipeline will evaluate the assembly quality of provided assembled contigs.

Please see the documentation for more information about the evaluate command.

Command

proksee evaluate -o output/directory CONTIGS

Where the argument provided after -o lets a user to specify a desired output directory. CONTIGS are FASTA-format assembled contigs.

Example

proksee evaluate -o output assembly.fasta

Contact

Eric Enns: eric.enns@canada.ca

Legal

Copyright Government of Canada 2020-2021

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.