:: DESCRIPTION
RNF (Read Naming Format) is a generic format for assigning names to simulated Next-Generation Sequencing (NGS) reads.
RNFtools is an associated software package for RNF
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
RNF: a general framework to evaluate NGS read mappers.
B?inda K, Boeva V, Kucherov G.
Bioinformatics. 2015 Sep 9. pii: btv524.
:: DESCRIPTION
NGS-Motif-Power is intended to calculate the p-value for pattern occurrences and the power of detecting enriched patterns in NGS reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhiyuan Zhai, Gesine Reinert, Kai Song, Michael S. Waterman, Yihui Luan, and Fengzhu Sun (2012)
Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads.
Journal of Computational Biology.
In press.
:: DESCRIPTION
Wombac rapidly finds core genome SNPs from samples and produces an alignment of those SNPs which can be used to build a phylogenomic tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Claire Lemaitre, Liviu Ciortuz and Pierre Peterlongo,
Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads
Proceedings of AlCoB 2014, in Algorithms for Computational Biology, LNCS vol. 8542, pp. 119–130.
:: DESCRIPTION
NextGenMap/NGM (Next Generation Mapper)is a computer program to map NGS reads against a reference genome using CPUs or GPUs.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468.
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Sedlazeck FJ, Rescheneder P, von Haeseler A.
