HTSeq 0.13.5 – Process and Analyze data from High-throughput Sequencing (HTS) Assays

HTSeq 0.13.5

:: DESCRIPTION

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HTSeq

:: MORE INFORMATION

Citation

HTSeq–a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W.
Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638.

ChIPseqR 1.46.0 – Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR 1.46.0

:: DESCRIPTION

ChIPseqR is an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ChIPseqR

:: MORE INFORMATION

Citation

ChIPseqR: analysis of ChIP-seq experiments.
Humburg P, Helliwell CA, Bulger D, Stone G.
BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.

BTP 1.0 – Analyzing Intra-tumor Heterogeneity from High-throughput Sequencing data

BTP 1.0

:: DESCRIPTION

BTP (Binary Tree Partition)is a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 BTP

:: MORE INFORMATION

Citation:

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Hajirasouliha I, Mahmoody A, Raphael BJ.
Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.

QuantumClone 1.0.0.6 – Clustering Mutations using High Throughput Sequencing (HTS) Data

QuantumClone 1.0.0.6

:: DESCRIPTION

QuantumClone is a clonal reconstruction method for whole genome or whole exome sequencing data.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R

:: DOWNLOAD

QuantumClone 

:: MORE INFORMATION

Citation

Deveau P, et al.
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.
Bioinformatics. 2018 Jun 1;34(11):1808-1816. doi: 10.1093/bioinformatics/bty016. PMID: 29342233; PMCID: PMC5972665.

REDseq 1.36.0 – Analysis of High-throughput Sequencing data processed by Restriction Enzyme Digestion

REDseq 1.36.0

:: DESCRIPTION

REDseq includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

 REDseq

:: MORE INFORMATION

Citation:

Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG.
Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo.
BMC Genomics. 2014 Dec 15;15(1):1104. doi: 10.1186/1471-2164-15-1104. PMID: 25494698; PMCID: PMC4378318.

pRESTO 0.5.13 – Processing raw reads from high-throughput Sequencing of Lymphocyte Repertoires

pRESTO 0.5.13

:: DESCRIPTION

pRESTO (REpertoire Sequencing TOolkit) is an integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Biopython
  • MUSCLE

:: DOWNLOAD

 pRESTO

:: MORE INFORMATION

Citation

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.
Vander Heiden JA, Yaari G, Uduman M, Stern JN, O’Connor KC, Hafler DA, Vigneault F, Kleinstein SH.
Bioinformatics. 2014 Mar 26.

GPSeq 0.5 – Using the Generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments

GPSeq 0.5

:: DESCRIPTION

GPSeq is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.

:: DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package/Perl/C Compiler

:: DOWNLOAD

 GPSeq

:: MORE INFORMATION

Citation:

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Srivastava S, Chen L.
Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670.

eXpress 1.5.3 – Streaming Quantification for High-throughput Sequencing

eXpress 1.5.3

:: DESCRIPTION

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm [1] that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

 eXpress

:: MORE INFORMATION

Citation

Roberts A and Pachter L (2012).
Streaming fragment assignment for real-time analysis of sequencing experiments.
Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251.

BOOGIE – Predicting Blood Groups from High Throughput Sequencing Data

BOOGIE

:: DESCRIPTION

BOOGIE is a fast predictor for the inference of blood groups from single nucleotide variant (SNV) databases.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BOOGIE

:: MORE INFORMATION

Citation

BOOGIE: Predicting Blood Groups from High Throughput Sequencing Data.
Giollo M, Minervini G, Scalzotto M, Leonardi E, Ferrari C, Tosatto SC.
PLoS One. 2015 Apr 20;10(4):e0124579. doi: 10.1371/journal.pone.0124579.

UEA sRNA Workbench 4.6 ALPHA – Analysing micro RNA and other small RNA data from High-Throughput Sequencing devices

UEA sRNA Workbench 4.6 ALPHA

:: DESCRIPTION

The UEA sRNA workbench is a new simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample sRNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

UEAsRNA

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Java 

:: DOWNLOAD

 UEA sRNA Workbench

:: MORE INFORMATION

Citation

Stocks, M. B.; Moxon, S.; Mapleson, D.; Woolfenden, H. C.; Mohorianu, I.; Folkes, L.; Schwach, F.; Dalmay, T. & Moulton, V. (2012)
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets.
Bioinformatics ,Vol. 28,pp. 2059-2061

RNA Biol. 2013 Jul;10(7):1221-30. doi: 10.4161/rna.25538. Epub 2013 Jun 28.
CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.
Mohorianu I1, Stocks MB, Wood J, Dalmay T, Moulton V.