PerM 0.4.0 – Read-mapping software based on Periodic Spaced Seeds for both Illumina and SOLiD sequencing data

PerM 0.4.0

:: DESCRIPTION

PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PerM

:: MORE INFORMATION

Citation:

Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.

BitSeq 0.7.5 / for R 1.36.0 – Bayesian Inference of Transcripts from Sequencing Data

BitSeq 0.7.5 / for R 1.36.0

:: DESCRIPTION

BitSeq is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

:: DEVELOPER

Peter Glaus , Antti Honkela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • GCC / BioCOnductor/ R package
  • Python

:: DOWNLOAD

 BitSeq / for R

:: MORE INFORMATION

Citation

Fast and accurate approximate inference of transcript expression from RNA-seq data.
Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.
Bioinformatics. 2015 Aug 26. pii: btv483

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.
Identifying differentially expressed transcripts from RNA-seq data with biological variation.
Glaus P, Honkela A, Rattray M.

HARSH 0.21 – Haplotype Inference using Reference and Sequencing Data

HARSH 0.21

:: DESCRIPTION

HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 HARSH

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386.
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

TIgGER 0.4.0 – Infers Novel Immunoglobulin Alleles from Sequencing Data

TIgGER 0.4.0

:: DESCRIPTION

TIgGER (Tool for Ig Genotype Elucidation via airR-seq) is a set of methods for identifying novel V gene alleles and constructing subject-specific genotypes.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

TIgGER

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A, 112 (8), E862-70 2015 Feb 24
Automated Analysis of High-Throughput B-cell Sequencing Data Reveals a High Frequency of Novel Immunoglobulin V Gene Segment Alleles
Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH.

npSeq 1.1.1 – Significance Analysis of Sequencing data

npSeq 1.1.1

:: DESCRIPTION

npSeq is an R package for the significance analysis of sequencing data.  The statistic used by npSeq is exactly the same as that in SAM 4.0. The only difference is that npSeq uses symmetric cutoffs, while SAM uses asymmetric cutoffs. Therefore, for some datasets, all significant genes obtained by SAM are either all up-regulated or all down-regulated, but npSeq almost always gives significant genes that include both up-regulated genes and down-regulated genes.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • R Package

:: DOWNLOAD

 npSeq

:: MORE INFORMATION

Citation

Jun Li and Robert Tibshirani (2011)
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
Stat Methods Med Res. 2011 Nov 28.

fineSTRUCTURE 4.0.1 – Identify Population Structure using Dense Sequencing Data

fineSTRUCTURE 4.0.1

:: DESCRIPTION

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.  By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals.

::DEVELOPER

Daniel Lawson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows with  MinGW/ MacOsX

:: DOWNLOAD

  fineSTRUCTURE

:: MORE INFORMATION

Citation

Lawson, Hellenthal, Myers, and Falush (2012),
Inference of population structure using dense haplotype data“,
PLoS Genetics, 8 (e1002453).

CAGEr 1.28.0 – Analysis of CAGE (Cap Analysis of Gene Expression) Sequencing Data

CAGEr 1.28.0

:: DESCRIPTION

CAGEr is an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 CAGEr

:: MORE INFORMATION

Citation

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.
Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B.
Nucleic Acids Res. 2015 Feb 4. pii: gkv054.

VARIFI – Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

VARIFI

:: DESCRIPTION

VARIFI is a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)).

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.
Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.
J Pers Med. 2019 Feb 1;9(1). pii: E10. doi: 10.3390/jpm9010010.

CircTest 0.1.0 / DCC 0.3.2 – Identification and Quantification of Circular RNAs from Sequencing Data

CircTest 0.1.0 / DCC 0.3.2

:: DESCRIPTION

CircTest tests the variation of circRNAs in respect to host genes.

DCC (detect circRNAs from chimeric reads) is a python package intended to detect and quantify circRNAs with high specificity.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • Python

:: DOWNLOAD

 CircTest , DCC

:: MORE INFORMATION

Citation

Specific identification and quantification of circular RNAs from sequencing data.
Cheng J, Metge F, Dieterich C.
Bioinformatics. 2015 Nov 9. pii: btv656