PgSA 1.2 – Index allowing Queries for a collection of Sequencing Reads

PgSA 1.2

:: 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

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PgSA

:: 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.

TAMER 1.0 – Taxonomic Assignment of Metagenomic Sequencing Reads

TAMER 1.0

:: DESCRIPTION

TAMER is an R package for accurate taxonomic assignment of metagenomic sequencing reads.

::DEVELOPER

Lingling An , Hongmei Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • R

:: DOWNLOAD

 TAMER

:: 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.

WhatsHap – Haplotype Assembly for Future-Generation Sequencing Reads

WhatsHap

:: 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

  • Linux
  • Python
  • C++

:: DOWNLOAD

 WhatsHap

:: 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

Bmap – Efficient and Error-tolerant Sequencing Read Mapping

Bmap

:: 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

  • Linux
  • Python

:: DOWNLOAD

 Bmap

:: MORE INFORMATION

IPED v1 – Sequencing Error Correction in 16S rRNA Illmina paired-end Sequencing Reads

IPED v1

:: 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

  • Linux

:: DOWNLOAD

 IPED

:: MORE INFORMATION

HMM-FRAME 20140724 – Protein Domain Classification for Sequencing Reads with Frameshift Errors

HMM-FRAME 20140724

:: 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

HMM-FRAME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • G++

:: DOWNLOAD

 HMM-FRAME

:: 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.

TreqCG 0.3 – Clustering Accelerates High-Throughput Sequencing Read Mapping

TreqCG 0.3

:: 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

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 TreqCG

:: MORE INFORMATION

Citation

Mahmud, Md and Schliep, Alexander.
TreQ-CG: Clustering Accelerates High-Throughput Sequencing Read Mapping (2014)

GeneSeq 1.0 – LD-based Genotype Calling from Shotgun Sequencing Reads

GeneSeq 1.0

:: 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

  • Linux

:: DOWNLOAD

GeneSeq

:: 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

AmosCmp16Spipeline 20090918 – Assemble 16S rRNA Sequencing Reads

AmosCmp16Spipeline 20090918

:: DESCRIPTION

AmosCmp16Spipeline uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AmosCmp16Spipeline

:: MORE INFORMATION

Citation

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW.
Genome Res. 2011 Mar;21(3):494-504. Epub 2011 Jan 6.