:: DESCRIPTION
TreqCG is a method to accelerate and improve read mapping based on an initial clustering of up to billions of high-throughput sequencing reads yielding clusters of high stringency and a high degree of overlap.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mahmud, Md and Schliep, Alexander.
TreQ-CG: Clustering Accelerates High-Throughput Sequencing Read Mapping (2014)
:: DESCRIPTION
HMM-FRAME is a protein domain classification tool based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. HMM-FRAME corrects sequencing errors and classifies putative gene fragments into domain families. It achieved high error detection sensitivity and specificity in a data set with annotated errors.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 May 24;12:198. doi: 10.1186/1471-2105-12-198.
HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors.
Zhang Y, Sun Y.
:: DESCRIPTION
IPED is a highly efficient denoising tool for Illumina paired-end 16S rRNA amplicon sequencing data.
::DEVELOPER
The Bioinformatics team of the Microbiology Unit, SCK.CEN
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Bmap is a tool for efficient and error-tolerant sequencing read mapping.
:: DEVELOPER
Computational and Systems Biology Group at the Faculty of Mathematics, Informatics and Mechanics, University of Warsaw
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TAMER is an R package for accurate taxonomic assignment of metagenomic sequencing reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(10):e46450. doi: 10.1371/journal.pone.0046450. Epub 2012 Oct 1.
A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.
Jiang H1, An L, Lin SM, Feng G, Qiu Y.
:: DESCRIPTION
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
::DEVELOPER
The Algorithms for Computational Genomics group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.
J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157
:: DESCRIPTION
PgSA (Pseudogenome Suffix Array) is a compact index for collections of reads from sequencing. It allows to ask for presence of k-mers in the reads.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2015 Jul 16;10(7):e0133198. doi: 10.1371/journal.pone.0133198. eCollection 2015.
Indexing Arbitrary-Length k-Mers in Sequencing Reads.
Kowalski T, Grabowski S, Deorowicz S.
:: DESCRIPTION
GeneSeq package provides methods to call SNP genotypes and infer haplotypes for a single individual given reads produced by whole-genome shotgun sequencing using high-throughput technologies such as 454, Illumina, and ABI SOLiD. GeneSeq yields high genotype calling accuracy even from low read coverage by ecploting linkage disequilibrium patterns extracted from a reference panel such as those generated by the international Hapmap project. Genotype and haplotype inference is performed efficiently using a hierarchical factorial hidden Markov model (HF-HMM) integrating allele coverage information extracted from read data with haplotype frequencies inferred from the reference panel.
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu,
Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads,
BMC Bioinformatics 12(Suppl 1):S53, 2011
