The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools. Remarque Please cite the following article if you use BEDTools in your research:
Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
This novel version of i-ADHoRe is designed to detect genomic homology in extremely large-scale data sets. Along with several under-the hood-improvements, resulting in a 30 fold reduction in runtime over previous versions, the
implementation of multithreading and MPI now enables i-ADHoRe to take advantage of a parallel computing platform. As the scale of the data sets increased, the need for a new alignment algorithm able to cope with dozens of genomic
segments became apparent. Therefore a new greedy graph based alignment algorithm has been implemented (described in Fostier et al., 2011), allowing analysis of even the largest data sets currently available.
|Run Unix # i-adhore||Run Web #|
Pandoc is a free and open-source software document converter, widely used as
a writing tool and as a basis for publishing workflows.
Pandoc can convert documents in markdown, reStructuredText, textile, HTML,
DocBook, LaTeX, MediaWiki markup, TWiki markup, OPML, Emacs Org-Mode,
Txt2Tags, Microsoft Word docx, LibreOffice ODT, EPUB, or Haddock markup to
HTML formats: XHTML, HTML5, and HTML slide shows using Slidy, reveal.js,
Slideous, S5, or DZSlides.
Word processor formats: Microsoft Word docx, OpenOffice/LibreOffice ODT,
Ebooks: EPUB version 2 or 3, FictionBook2
Documentation formats: DocBook, GNU TexInfo, Groff man pages, Haddock
Page layout formats: InDesign ICML
Outline formats: OPML
TeX formats: LaTeX, ConTeXt, LaTeX Beamer slides
PDF via LaTeX
Lightweight markup formats: Markdown (including CommonMark),
reStructuredText, AsciiDoc, MediaWiki markup, DokuWiki markup, Emacs
Custom formats: custom writers can be written in lua.Remarque
|Run Unix # pandoc [OPTIONS] [FILES]
||Run Web #|
QPDF is a command-line program that does structural, content-preserving transformations on PDF files. It could have been called something like pdf-to-pdf. It also provides many useful capabilities to developers of PDF-producing software or for people who just want to look at the innards of a PDF file to learn more about how they work. Remarque
|Run Unix # qpdf [options] infile outfile||Run Web #|
quantiNEMO is an individual-based, genetically explicit stochastic
simulation program. It was developed to investigate the effects of
selection, mutation, recombination, and drift on quantitative traits with
varying architectures in structured populations connected by migration and
located in a heterogeneous habitat. quantiNEMO is highly flexible at various
levels: population, selection, trait(s) architecture, genetic map for QTL
and/or markers, environment, demography, mating system, etc.
|Run Unix # quantiNemo||Run Web #|
Easy identification and removal of rRNA-like sequences.
The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
|Run Unix # ribopicker [options] -f -dbs |
|Run Web #|
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity. Remarque If you use SortMeRNA, please cite:
Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.
|Run Unix # sortmerna -h
||Run Web #|
Subtilis Protein interaction DatabaseRemarque
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format (Note that this is not required for submission). The Toolkit source code is provided in the form of the SRA SDK, and may be compiled with GCC. However, pre-built software executables are available for Linux, Windows, and Mac OS X, and we highly recommend using these pre-built executables whenever possible.Remarque