项目作者: aquaskyline

项目描述 :
10x Genomics Reads Simulator
高级语言: C
项目地址: git://github.com/aquaskyline/LRSIM.git
创建时间: 2016-11-19T23:37:20Z
项目社区:https://github.com/aquaskyline/LRSIM

开源协议:MIT License

下载


LRSIM: Simulator for Linked Reads

DOI

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.

Getting Started

  1. git clone --recursive https://github.com/aquaskyline/LRSIM.git
  2. cd LRSIM
  3. sh make.sh
  4. cd test
  5. sh test.sh

Tips to run

  1. Please review the 10X Genomics website for an overivew of the sequencing process and the definitions of the related terms. Note that ‘Molecule’ and ‘Partition’ are synonymous to ‘Fragment’ and ‘Pool’.
  2. If you encounter the “Missing Inline::C library” error, please install the Inline::C perl library using CPAN or uncomment the following two lines of code by removing the hash symbol at the front.
    1. #use lib "./lib";
    2. #use lib dirname($0)."/lib";
  3. The simulated reads were tested to be compaitible with “longRanger wgs” and “supernova”.
  4. The default parameters are similar to 10X Chromium’s standard protocal for human genome.
  5. Set -z to run DWGSIM in parallel. For the human genome, each copy of DWGSIM takes 4GB memory. Set -z to the number of available cores if you have enough memory.
  6. For the human genome, the memory consumption peaks at 48GB, and takes about 5 hours to finish with default parameters.
  7. With the same output prefix -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.
  8. Please use this pipeline for non-human genomes at your own risk. You may want to use -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).
  9. I hate asking users to install dependencies, so they are included in the repo (make sure to use git clone —recursive). If you still run into problem, please write to me.
  10. To simulate reads using known variants, please provide LRSIM with variant inserted haploid FASTA files using -g, separated by comma. I suggest using vcf2diploid to generate haploid FASTAs from VCF.
  11. User can provide ia real fragment size distribution using -c. A sample file is at test/fragmentSizesList.

Parameters

  1. Usage: ./simulateLinkedReads.pl -r/-g <reference/haplotypes> -p <output prefix> [options]
  2. Reference genome and variants:
  3. -d INT Haplotypes to simulate [2]
  4. -g STRING Haploid FASTAs separated by comma. Overrides -r and -d.
  5. -1 INT 1 SNP per INT base pairs [1000]
  6. -2 INT Minimum length of Indels [1]
  7. -3 INT Maximum length of Indels [50]
  8. -4 INT # of Indels [1000]
  9. -5 INT Minimum length of Duplications and Inversions [1000]
  10. -6 INT Maximum length of Duplications and Inversions [10000]
  11. -7 INT # of Duplications and # of Inversions [100]
  12. -8 INT Minimum length of Translocations [1000]
  13. -9 INT Maximum length of Translocations [10000]
  14. -0 INT # of Translocations [100]
  15. Illumina reads characteristics:
  16. -e FLOAT Per base error rate of the first read [0.0001,0.0016]
  17. -E FLOAT Per base error rate of the second read [0.0001,0.0016]
  18. -i INT Outer distance between the two ends for pairs [350]
  19. -s INT Standard deviation of the distance for pairs [35]
  20. Linked reads parameters:
  21. -b STRING Barcodes list
  22. -x INT # million reads pairs in total to simulated [600]
  23. -f INT Mean molecule length in kbp [100]
  24. -c STRING Input a list of fragment sizes. Overrrides -f.
  25. -t INT n*1000 partitions to generate [1500]
  26. -m INT Average # of molecules per partition [10]
  27. Miscellaneous:
  28. -u INT Continue from a step [auto]
  29. 1. Variant simulation
  30. 2. Build fasta index
  31. 3. DWGSIM
  32. 4. Simulate reads
  33. 5. Sort reads extraction manifest
  34. 6. Extract reads
  35. -z INT # of threads to run DWGSIM [8]
  36. -o Disable parameter checking
  37. -h Show this help

The ratio of homozygous to heterzygous simulated variant is hardcoded as 1:2.

Acknowledgement

The simulator uses a modified version of DWGSIM originally developed by Nils Homer (nh13/DWGSIM) and SURVIVOR by Fritz Sadlezeck (fritzsedlazeck/SURVIVOR).

License

  1. The MIT License (MIT)
  2. Copyright (c) 2016 Ruibang Luo <aquaskyline@gmail.com>
  3. Permission is hereby granted, free of charge, to any person obtaining a copy
  4. of this software and associated documentation files (the "Software"), to deal
  5. in the Software without restriction, including without limitation the rights
  6. to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  7. copies of the Software, and to permit persons to whom the Software is furnished
  8. to do so, subject to the following conditions:
  9. The above copyright notice and this permission notice shall be included in all
  10. copies or substantial portions of the Software.
  11. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  12. IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  13. FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  14. AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
  15. WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
  16. CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.