10x Genomics Reads Simulator
This package simulates whole genome sequencing using 10X Genomics Linked Read technology. We have attempted to realistically capture all of the relevant steps of the 10X protocol so that it can be used to faithfully evaluate linked read sequencing of different genomes, mutation rates, input libraries, and short read sequencing conditions in silico. We have tested the package with LongRanger, SuperNova, HapCUT2, fragScaff and ARCS to confirm that variant identifation, phasing, de novo assembly and scaffolding are supported. We also encourage users to use these simulations to aid in the development of novel algorithms. Please feel free to contact us if your pipelines require additional features.
git clone --recursive https://github.com/aquaskyline/LRSIM.git
cd LRSIM
sh make.sh
cd test
sh test.sh
#use lib "./lib";
#use lib dirname($0)."/lib";
-p
, you can continue from step 4: Simulate reads using option -u 4
with different -f
(fragment size), -t
(partitions to generate) and -m
(average number of molecules per partition). This shortern the simulation from 5 hours to 1.5 hours for human.-o
to skip valid range check on parameters. You shouldn’t set -m
to over 4700, which is the number of available barcodes, or the program will not run to the end. Note that the default barcoding parameters do not perform well for small genomes (<100Mbp).-g
, separated by comma. I suggest using vcf2diploid to generate haploid FASTAs from VCF.-c
. A sample file is at test/fragmentSizesList
.
Usage: ./simulateLinkedReads.pl -r/-g <reference/haplotypes> -p <output prefix> [options]
Reference genome and variants:
-d INT Haplotypes to simulate [2]
-g STRING Haploid FASTAs separated by comma. Overrides -r and -d.
-1 INT 1 SNP per INT base pairs [1000]
-2 INT Minimum length of Indels [1]
-3 INT Maximum length of Indels [50]
-4 INT # of Indels [1000]
-5 INT Minimum length of Duplications and Inversions [1000]
-6 INT Maximum length of Duplications and Inversions [10000]
-7 INT # of Duplications and # of Inversions [100]
-8 INT Minimum length of Translocations [1000]
-9 INT Maximum length of Translocations [10000]
-0 INT # of Translocations [100]
Illumina reads characteristics:
-e FLOAT Per base error rate of the first read [0.0001,0.0016]
-E FLOAT Per base error rate of the second read [0.0001,0.0016]
-i INT Outer distance between the two ends for pairs [350]
-s INT Standard deviation of the distance for pairs [35]
Linked reads parameters:
-b STRING Barcodes list
-x INT # million reads pairs in total to simulated [600]
-f INT Mean molecule length in kbp [100]
-c STRING Input a list of fragment sizes. Overrrides -f.
-t INT n*1000 partitions to generate [1500]
-m INT Average # of molecules per partition [10]
Miscellaneous:
-u INT Continue from a step [auto]
1. Variant simulation
2. Build fasta index
3. DWGSIM
4. Simulate reads
5. Sort reads extraction manifest
6. Extract reads
-z INT # of threads to run DWGSIM [8]
-o Disable parameter checking
-h Show this help
The ratio of homozygous to heterzygous simulated variant is hardcoded as 1:2.
The simulator uses a modified version of DWGSIM originally developed by Nils Homer (nh13/DWGSIM) and SURVIVOR by Fritz Sadlezeck (fritzsedlazeck/SURVIVOR).
The MIT License (MIT)
Copyright (c) 2016 Ruibang Luo <aquaskyline@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is furnished
to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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