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NeSSM specifications


Unique identifier OMICS_01510
Name NeSSM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Chaochun Wei <>

Publication for NeSSM

NeSSM in publications

PMCID: 4892715
PMID: 27162180
DOI: 10.1093/femsec/fiw095

[…] will quantify the accuracy of these programs for annotating sequences from organisms whose genomes are stored in the ncbi databases., a simulated metagenome, hereafter simmet, was created using nessm (jia et al. ), comprising the complete ncbi bacterial genome database (, may 2013 collection, accessed on 29/04/14). nessm creates […]

PMCID: 4628670
PMID: 26557648
DOI: 10.1155/2015/197895

[…] clusters more correctly., though there is no generally acknowledged benchmark for binning ngs reads at present, several tools are recently proposed for simulating metagenomics, such as art [], nessm [], bear [], and metasim []. our binning method is based on the one-dimensional ca (1d-ca) to automatically determine the clusters for reads, and to validate it, the dataset as the work in [] […]

PMCID: 4533152
PMID: 26200428
DOI: 10.7554/eLife.08490.023

[…] nc_002655 nc_002662 nc_002695 nc_002935 nc_003030 nc_003212 nc_003295 nc_003366 nc_003997 nc_004070 nc_004307 nc_004310 nc_004431 nc_004557 nc_004567 nc_004668 nc_004722 nc_005085 nc_005362). nessm () was used to simulated hiseq illumina reads (100 bp paired-ends) with a coverage of the prophage region varying between 5×, 25×, 50×, 75×, and 100×. reads were then assembled with idba_ud (), […]

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NeSSM institution(s)
School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
NeSSM funding source(s)
This work was supported by grants from the National Natural Science Foundation of China (61272250), the National Basic Research Program of China (2012AA101601, 2012CB316501), and the National High-Tech R&D Program (2012AA101601).

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