MixAmp: Amplicon Read Simulator

A tool for Amplicon read simulation for waste water sequencing or other aplications. Users can easily simulate reads from mutiple samples with different proportions using the tool.

Usage

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) https://github.com/andersen-lab/MixAmp repository.

Installation

Please follow these steps to install required dependencies:

1. pip install git+https://github.com/andersen-lab/MixAmp
2. Install dependencies in an activated conda environment:

conda env update --file environment.yml

Example commands

• Run the tool using the following command.

   mixamp simulate-proportions [SAMPLE1.fasta,SAMPLE2.fasta,..] [primer.bed] --proportions [0.8,0.2,..] --outdir [output_directory]

Imagine we have two different samples with their whole genome fasta files and we are trying to simulate reads from these two.

• Simulate reads without defining proportions (will be assigned randomly, proportions can be found in results/sample_proportions.txt)

   mixamp simulate-proportions sample.fasta,sample2.fasta primer.bed --outdir results/

• Simulate reads with user-defined proportions.

   mixamp simulate-proportions sample.fasta,sample2.fasta primer.bed --proportions 0.2,0.8

• Simulate reads with user-defined proportions and total number of reads.

   mixamp simulate-proportions sample.fasta,sample2.fasta primer.bed --proportions 0.2,0.8 --readcnt 20000

• Simulate reads with additional parameters such as base error rate, read length and indels fraction

   mixamp simulate-proportions sample.fasta,sample2.fasta primer.bed --proportions 0.2,0.8 --readcnt 20000 --error_rate 0.001 --read_length 400 --indel_fraction 0.001

Notes

• Please remember that the primer file must contain a column containing primer sequence. The maximum number of mismatches allowed for each primer sequence is 1 SNP. To change this number, you may use the --maxmismatches flag.

• To learn more about how to adjust other parameters use mixamp simulate-proportions --help

• Simulated reads from all samples are located in provided_output_path/reads.fastq

• The pipeline will automatically generate random proportions if not provided by the user.

• In order to find more about amplicon dropouts, please refer to provided_output_path/sample_name/amplicon_stats.csv file.

• If there are no right or left primer match, the start/end and length of the amplicon will equal to zero.