SIGs/SciTech/BioinformaticsWishList

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(Alphabetical sort)
(Added links to review requests for bwa and fastx_toolkit)
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* [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment
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* [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment - see [https://bugzilla.redhat.com/show_bug.cgi?id=597315]
 
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
 
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
 
* <strike>[http://emboss.sourceforge.net/ EMBOSS] - Hundreds of useful, well documented applications for molecular sequence and other analyses.</strike>
 
* <strike>[http://emboss.sourceforge.net/ EMBOSS] - Hundreds of useful, well documented applications for molecular sequence and other analyses.</strike>
* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing
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* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing - see [https://bugzilla.redhat.com/show_bug.cgi?id=597307]
 
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
 
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
 
* [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
 
* [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.

Revision as of 16:06, 28 May 2010

  • bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment - see [1]
  • Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
  • EMBOSS - Hundreds of useful, well documented applications for molecular sequence and other analyses.
  • FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing - see [2]
  • GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
  • MIRA - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
  • NCBI BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
  • NCBI C Toolkit - NCBI libraries and tools for biology applications srpm here
  • NCBI C++ Toolkit - a new generation of NCBI libraries and tools for biology
  • pyQPCR - qPCR analysis tool
  • SAMtools - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
  • Staden - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
  • Taverna - Tool for automation of experimental workflows.