Very simple simulation of sequences with random mutations, and simulating linked-read (https://www.10xgenomics.com/linked-reads/) sequencing FASTQ data using LRTK-SIM.
To simulate sequences with random mutations, first a FASTA sequence is mutated randomly with bin/mutate_fasta.py, and then bin/make_haps.py shuffles these mutations randomly, creating FASTA seqences with random mutations.
The LRTK-SIM/LRTK-SIM.py script from zhanglu295/LRTK-SIM is used to simulate linked reads from the FASTA haplotypes.
zhanglu295/LRTK-SIM
LRTK-SIM is included as a submodule, so use --recursive when cloning this repo:
git clone --recursive https://github.com/olavurmortensen/linkedsim.git