SimSeq specifications

Information


Unique identifier OMICS_00258
Name SimSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Programming languages Java
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for SimSeq

SimSeq in publications

 (7)
PMCID: 5884625
PMID: 29554130
DOI: 10.1371/journal.ppat.1006882

[…] genomes of e. histolytica, which were deposited into the genbank database as follows. to construct simulated paired-end reads from the available genomic sequences of seven e. histolytica strains, simseq software [] was used with the following default parameter modifications: 14,000,000 paired-end reads, mean insert size of 200 mer, read length of 150 mer, and no mutations model. the short […]

PMCID: 5349696
PMID: 28192431
DOI: 10.1371/journal.pntd.0005386

[…] and sickle (https://github.com/najoshi/sickle) program. simulated paired-end reads were constructed from the available genomic sequences of v. cholerae strains using simseq software [] with the following parameter: number of pairs of reads, ‘‘read_number 2000000”; mean library insert size, ‘‘insert_size 150”; and paired-end reads length of 120 mer, ‘‘21 120 22 […]

PMCID: 4769523
PMID: 26920804
DOI: 10.1186/s12864-016-2463-2

[…] but real samples may also contain true minor alleles which are then falsely considered to be sequence errors, thereby skewing the evaluation of the method. the simulated sequences were generated by simseq. [] in brief, thirteen complete mtdna genome sequences representing the major haplogroups in modern humans were downloaded from ncbi and used as the templates for simulated reads (see methods […]

PMCID: 4263727
PMID: 25503461
DOI: 10.1371/journal.pone.0114848

[…] genes covers at least 80% between m. massiliense jcm 15300 and other mycobacterium spp., to construct simulated paired-end reads from the available genomic sequences of m. abscessus group strains, simseq software was used with “simseq.jar” and “samtofastq.jar” commands with the following default parameter modifications: number of pairs of reads, “—read_number 2000000”; mean library insert […]

PMCID: 3607606
PMID: 23536903
DOI: 10.1371/journal.pone.0060058

[…] lists as a canonical set in order to assess bubbleparse performance. in a separate experiment, we created a simulated mutant of the e. coli genome containing 100,000 randomly positioned snps. using simseq, a tool created for the assemblathon project , we produced 76 nt simulated illumina reads of the reference e. coli and the mutant at approximately 20× coverage and using simseq's supplied […]


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SimSeq institution(s)
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA

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