ipyrad2 0.1.9

Interactive assembly and analysis of RAD-seq data sets

ipyrad

Integrative assembly and analysis of RAD-seq datasets

Documentation

Draft documentation now lives in docs/ and is configured by zensical.toml.

To preview the docs locally with Zensical:

zensical serve

Usage

# help message for subcommand options
ipyrad2 -h

The core command-line arguments:

# demultiplex reads by barcode/index to sample files
ipyrad2 demux -d DATA/*.fastq.gz -b barcodes.tsv -o FASTQs/ -c 10 -t 2

# quality, adapter, and restriction overhang trimming
ipyrad2 trim -d FASTQs/*fastq.gz -o TRIMMED/ -c 10 -t 2

# map reads to reference genome to get filtered/sorted/marked bams
ipyrad2 map -d TRIMMED/*.fastq.gz -r REF.fa -o BAMs/ -c 10 -t 2

# assemble loci and call variants
ipyrad2 assemble -d BAMs/*.bam -r REF.fa -o OUT/ -m 4 -d 5 -c 10 -t 2

Installation

# clone the development repo
git clone ...

# install dependencies
cd ipyrad2/
conda env create -f environment.yml -n ipyrad2
conda activate

# install local dev copy of ipyrad2
pip install -e . --no-deps