Question: Simulating sanger sequence reads with mason
gravatar for africys
6.0 years ago by
africys0 wrote:

I am trying to simulate sanger sequencing reads with mason. The idea is to used mason to generate random snps based on a provided error.


 mason sanger --read-length-error 0.1

I am not sure what I am doing wrong but i get this error message

reference file: test.fasta
Loading reference sequence from "test.fasta"
Simulating for haplotype #0...
  Building haplotype...
    contig # 1/1    1.12    SNPs:0    indels:0    indel len sum:    0    vrate:0
  Finished haplotype creation in 0.000380993s
  Simulating reads for haplotype #0...
ERROR: haplotype (== 366) < read length!

What does this error mean? I could not find any documentation and description of mason error messages anywhere. Have you used mason

simulation assembly • 2.0k views
ADD COMMENTlink modified 5.9 years ago by Brian Bushnell17k • written 6.0 years ago by africys0
gravatar for Brian Bushnell
5.9 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

Unfortunately, I have little experience with Sanger data. The BBMap package has a read simulation tool, "RandomReads", which will generate synthetic reads of specified length ranges with specified error rates, paired or single-ended. It only has quality profiles for Illumina and PacBio, but if those are not sufficient, I would be happy to add a Sanger profile.

A typical command is something like this: ref=hg19.fa snprate=0.20 maxsnps=3 delrate=0.01 \
               maxdels=1 maxdellen=5 insrate=0.01 nrate=0.01 \
               minlen=200 maxlen=800 reads=100000 maxq=40 \
               midq=35 minq=25 out=reads.fq

...which would generate 100000 reads with lengths between 200 and 800bp. 20% would have at least 1 SNP; 20% of those 20% would have 2+ SNPs, etc. up to a max of 3, and various other mutations as listed. Each read's ID is its original unmutated genomic location so that you can determine absolutely where a read came from. It's highly customizable, and explains most of the details if you run the shell script with no arguments, but let me know if you have questions.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 5.9 years ago by Brian Bushnell17k
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