Package for HIV-1 env plasmid sequencing analysis with optimassembly.
envseq.sh is the main script for HIV-1 env plasmid sequencing analysis. First, it subtracts reads aligning to the backbone of the plasmid with smalt/samtools. Then it de novo assembles the insert using optimassembly. Default settings use pcDNA3 as a backbone vector and HXB2 as reference strain. Input is a directory containing gzipped fastq files. Output is a fast file SAMPLE_cons.fasta.
optimassembly.py is from ozagordi
pcDNA3_bb.fasta is the reference for the plasmid (backbone only!)
HXB2.fasta is the reference for HIV-1
To ensure you have all dependencies needed for EnvSeq installed you can use the environment.yml file.
First you need to have Conda installed).
With the command conda env create -f <path>/environment.yml you will create a copy of the EnvSeq environment.
You enter the environment with the command source activate EnvSeq (and leave it with source deactivate).
For more information visit following link to Managing environments.
usage: envseq.sh [options] ...
OPTIONS
-r, --reference reference (default HXB2.fasta)
-b, --backbone plasmid backbone to be subtracted (default pcDNA3_bb.fasta)
-n, --reads_limit limit number of reads (default 100'000)
-l, --expected_length expected insert length (default 3500)