:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
htSeqTools is a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies.
::DEVELOPER
Evarist Planet, Camille Stephan-Otto, Oscar Reina <oscar.reina at irbbarcelona.org>, Oscar Flores, David Rossell
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
htSeqTools: high-throughput sequencing quality control, processing and visualization in R.
Planet E, Attolini CS, Reina O, Flores O, Rossell D.
Bioinformatics. 2012 Feb 15;28(4):589-90. doi: 10.1093/bioinformatics/btr700.
:: DESCRIPTION
HapFlow is a python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
HapFlow: Visualising haplotypes in sequencing data.
Sullivan MJ, Bachmann NL, Timms P, Polkinghorne A.
Bioinformatics. 2015 Oct 7. pii: btv551.
:: 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
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
damidseq pipeline: an automated pipeline for processing DamID sequencing datasets.
Marshall OJ, Brand AH.
Bioinformatics. 2015 Jun 25. pii: btv386
:: DESCRIPTION
FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C (Circularized Chromosome Conformation Capture)sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FourCSeq: Analysis of 4C sequencing data.
Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W.
Bioinformatics. 2015 Jun 1. pii: btv335.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
vtools (variant tools) is a set of tools for annotating and tracking sequence variation for large-scale exome sequencing projects. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provide a whole set of tools to manipulate and analyze genetic variants.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Feb 1;28(3):421-2. Epub 2011 Dec 2.
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.
San Lucas FA, Wang G, Scheet P, Peng B.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
VDJtools is a comprehensive framework for post-analysis of immune repertoire sequencing data.
::DEVELOPER
Immuno-sequencing Algorithms Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
