nfixplanet 0.1.0

Nitrogen Fixer detection pipeline

NFixPlanet

Python package for detection of nitrogen fixers.

Description

TODO: need to update description TODO: mention somewhere that the pipeline only works for short read sequences (coverm step)

Installation

TODO: install via pip TODO: install via conda

Local installation

git clone [e-mail]:grp-bork/nfixplanet.git
cd nfixplanet
conda create -c bioconda -n nfixdev python=3.11 prodigal=2.6.3 hmmer=3.4 "defopt<7" wget hostile=2.0.0 fastp=0.24.0 minimap2=2.28 coverm=0.7.0
conda activate nfixdev
pip install -e .[dev]

Requirements:

• Prodigal V2.6.3: February, 2016
• HMMER 3.4 (Aug 2023); http://hmmer.org/

Usage

nfixplanet annotate

Pipeline for annotating genomes as N-fixers TODO: update description

Basic command:

nfixplanet annotate --input_fasta /path/to/fasta --output_directory /path/to/output

Optional arguments:

• --genomic_context_range <int>: Maximum number of genes upstream or downstream to consider for operon context (default: 10).
• --cpus <int>: Number of CPUs to use for HMMscan (default: 2, max recommended: 4).
• --verbose: Enable verbose (DEBUG) logging.
• --version: Print version number and exit.

nfixplanet map

Pipeline for mapping metagenomes TODO: update description

Basic command:

nfixplanet map \
  --sample_id SAMPLE_NAME \
  --read_1 /path/to/read_1.fastq \
  --read_2 /path/to/read_2.fastq \
  --single /path/to/reads.fastq \
  --output_directory /path/to/output

Required arguments:

• --sample_id <str>: Name of the FASTA/FASTQ sample.
• --output_directory <str>: Path to output directory.

Input read options (choose one mode):

• --read_1 <str>: Path to FASTA/FASTQ file for paired-end read 1 (R1).
• --read_2 <str>: Path to FASTA/FASTQ file for paired-end read 2 (R2). Must be provided together with --read_1.
• --single <str>: Path to FASTA/FASTQ file for single-end reads Can be used on its own or with --read_1 and --read_2.

Optional arguments:

• --work_directory <str>: Path to directory for temporary files (default: tmp).
• --cpus <int>: Number of CPUs used by processes (default: 8).
• --verbose: Enable verbose logging.

Authors and acknowledgment

• Mahdi Robbani
• Lucas Ustick
• Anthony Fullam

License

This project is licensed under the MIT License. See the LICENSE file for details.