Unconfigured Ad

**jts** · 03-30-2011, 02:07 AM

I use SimSeq by John St. John:

GitHub - jstjohn/SimSeq: An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

https://github.com/jstjohn/SimSeq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential f...

**steven** · 03-30-2011, 02:54 AM

You may want to try the Flux Simulator too

**suryasaha** · 03-30-2011, 05:49 AM

Samtools includes the wgsim read simulator. It will be in the samtools-XXXX/misc/ directory after you install Samtools.

Code:

Program: wgsim (short read simulator)
Version: 0.2.3
Contact: Heng Li <[email protected]>

Usage:   wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>

Options: -e FLOAT      base error rate [0.020]
         -d INT        outer distance between the two ends [500]
         -s INT        standard deviation [50]
         -N INT        number of read pairs [1000000]
         -1 INT        length of the first read [70]
         -2 INT        length of the second read [70]
         -r FLOAT      rate of mutations [0.0010]
         -R FLOAT      fraction of indels [0.10]
         -X FLOAT      probability an indel is extended [0.30]
         -c            generate reads in color space (SOLiD reads)
         -C            show mismatch info in comment rather than read name
         -h            haplotype mode

Note: For SOLiD reads, the first read is F3 and the second is R3.

**schönblick** · 03-30-2011, 06:45 AM

thanks all for suggestions!

**mdk308** · 09-20-2012, 09:06 AM

Originally posted by suryasaha View Post

Samtools includes the wgsim read simulator. It will be in the samtools-XXXX/misc/ directory after you install Samtools.

any idea how wgsim handles multifasta files? do i need to remove all of the headers or can i just run as is?

**lyz1030** · 09-20-2012, 09:39 AM

can anyone tell me how wgsim simulate variants (the position can be specified ) or we can get the variant position. The objective is to evaluate the false negative rate of variant calling softwares.

Topics	Statistics	Last Post
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 23 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2 Started by SEQadmin2, 06-30-2026, 05:37 AM	0 responses 23 views 0 reactions	Last Post by SEQadmin2 06-30-2026, 05:37 AM
Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2 Started by SEQadmin2, 06-26-2026, 11:10 AM	0 responses 23 views 0 reactions	Last Post by SEQadmin2 06-26-2026, 11:10 AM
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, 06-17-2026, 06:09 AM	0 responses 55 views 0 reactions	Last Post by SEQadmin2 06-17-2026, 06:09 AM

Unconfigured Ad

recommend a short reads simulator?

Comment

Comment

Comment

Comment

Comment

Comment

Latest Articles

ad_right_rmr

News