GenomeBrowse 2.1.2 – Free Genome Browser for Exploring Sequencing Pile-up

GenomeBrowse 2.1.2

:: DESCRIPTION

GenomeBrowse raises the bar on the experience of exploring and finding key insights into your genomic data. Every component has been designed and optimized to give you a user-experience beyond imagination.

::DEVELOPER

Golden Helix, Inc

:: SCREENSHOTS

GenomeBrowse

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GenomeBrowse

:: MORE INFORMATION

Heat*seq – High-throughput Sequencing Experiment Comparison with Public data

Heat*seq

:: DESCRIPTION

Heat*seq is a web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain.

::DEVELOPER

Heat*seq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Heat*seq

:: MORE INFORMATION

Citation:

Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data.
Devailly G, Mantsoki A, Joshi A.
Bioinformatics. 2016 Jul 4. pii: btw407.

DSS 2.12.0 – Dispersion Shrinakge for Sequencing data

DSS 2.12.0

:: DESCRIPTION

DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq).

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  DSS

:: MORE INFORMATION

Citation

Differential methylation analysis for BS-seq data under general experimental design.
Park Y, Wu H.
Bioinformatics. 2016 Jan 27. pii: btw026

Wu H, Wang C and Wu Z
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.
Biostat (2013) 14 (2): 232-243. http://dx.doi.org/10.1093/biostatistics/kxs033.

ParDRe 1.1.5 – Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies

ParDRe 1.1.5

:: DESCRIPTION

ParDRe is a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files.

::DEVELOPER

Jorge González Domínguez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ParDRe

:: MORE INFORMATION

Citation:

ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies.
González-Domínguez J, Schmidt B.
Bioinformatics. 2016 Jan 22. pii: btw038.

Lighter 1.1.1 – Fast and Memory-efficient Sequencing Error Correction without Counting

Lighter 1.1.1

:: DESCRIPTION

Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 Lighter

:: MORE INFORMATION

Citation

Genome Biol. 2014;15(11):509.
Lighter: fast and memory-efficient sequencing error correction without counting.
Song L, Florea L, Langmead B.

MiXCR 1.8.1 – Analysis of T- and B- cell Receptor Repertoire Sequencing data

MiXCR 1.8.1

:: DESCRIPTION

MiXCR is an universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

::DEVELOPER

MiLaboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JRE
:: DOWNLOAD

 MiXCR

:: MORE INFORMATION

Citation:

Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364.
MiXCR: software for comprehensive adaptive immunity profiling.
Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M3, Mamedov IZ, Putintseva EV, Chudakov DM.

VDJtools 1.0.9 – Post-analysis of Immune Repertoire Sequencing data

VDJtools 1.0.9

:: DESCRIPTION

VDJtools is a comprehensive framework for post-analysis of immune repertoire sequencing data.

::DEVELOPER

Mikhail Shugay

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • JRE
:: DOWNLOAD

 VDJtools

:: MORE INFORMATION

Citation:

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM.
PLoS Comput Biol. 2015 Nov 25;11(11):e1004503. doi: 10.1371/journal.pcbi.1004503.

Cpipe 2.2.0 – Exome Sequencing Pipeline

Cpipe 2.2.0

:: DESCRIPTION

Cpipe is a variant detection pipeline designed to process high throughput sequencing data (sometimes called “next generation sequencing” data), with the purpose of identifying potentially pathogenic mutations.

::DEVELOPER

the Melbourne Genomics Health Alliance

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 Cpipe

:: MORE INFORMATION

Citation:

Cpipe: a shared variant detection pipeline designed for diagnostic settings.
Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.
Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x.

CLAMMS – A CNV-calling algorithm for Exome Sequencing data

CLAMMS

:: DESCRIPTION

CLAMMS (Copy number estimation using Lattice-Aligned Mixture Models) is an algorithm for calling copy number variants (CNVs) from exome sequencing read depths.

::DEVELOPER

Regeneron Genetics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

CLAMMS

:: MORE INFORMATION

Citation:

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.
Packer JS, Maxwell EK, O’Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG.
Bioinformatics. 2015 Sep 17. pii: btv547.

damidseq_pipeline 1.4 – An automated pipeline for processing DamID Sequencing Datasets

damidseq_pipeline 1.4

:: DESCRIPTION

damidseq_pipeline (DamID-seq pipeline) is a single script that automatically handles sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation.

::DEVELOPER

Owen MarshallAndrea Brand

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Perl

:: DOWNLOAD

 damidseq_pipeline

:: MORE INFORMATION

Citation:

damidseq pipeline: an automated pipeline for processing DamID sequencing datasets.
Marshall OJ, Brand AH.
Bioinformatics. 2015 Jun 25. pii: btv386