AmpHap (Amplicons to Haplotypes) is a Python script designed for Linux-compatible operating systems, developed by various third-party programs including fastp, flash, seqtk, and fastx_toolkit. AmpHap takes as input the paired-end sequencing results in FASTQ format (RawReads_1.fastq, RawReads_2.fastq) and a file containing information of population-specific primers (primer.tab). AmpHap ultimately generates the haplotypes and their frequencies for targeted amplification regions of different populations in FASTA format.
fastp v0.23.2 (https://github.com/OpenGene/fastp)
FLASH v1.2.11 (https://github.com/dstreett/FLASH2)
seqtk v1.3-r106 (https://github.com/lh3/seqtk)
fastx_toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/)
- Program execution flow
- Conda environment
conda create -n AmpHap python=3.10 # python version 3.6+
conda acitvate AmpHap
conda install fastp flash seqtk fastx_toolkit
- Get AmpHap
git clone https://github.com/RoderickNi/AmpHap.git
python AmpHapMain.py
--RawFq1 Reads1.fq \ # Reads-2.fq
--RawFq2 Reads2.fq \ # Reads_1.fq
--Primers Primer.tab \ # Primer and Samp_Size information
--ReadType (string) \ # PE150 or PE250 (default: PE250)
--SeqLen (int) \ # Mean Length of Amplicon
--Bias (int) \ # Amplicon length variation permitted
--Regulation (int) \ # Increase or decrease the filtering threshold based on 1/2N (N:Sample Size)
--CPU (int)\ # Number of processors used