SIGs/SciTech/BioinformaticsWishList

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(Use the same style of Package_maintainers_wishlist for links to Review Requests)
(Add IGV: http://www.broadinstitute.org/igv/)
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* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing ([https://bugzilla.redhat.com/show_bug.cgi?id=597307 Review Request])
 
* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing ([https://bugzilla.redhat.com/show_bug.cgi?id=597307 Review Request])
 
* [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.broadinstitute.org/igv/ Integrated Genomics Viewer] - java-based graphical genomics viewer (licensed under GPLv2)
 
* [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.
 
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI BLAST and other tools]  - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
 
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI BLAST and other tools]  - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.

Revision as of 00:26, 3 June 2010

  • bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment (Review Request)
  • 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 (Review Request)
  • GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
  • Integrated Genomics Viewer - java-based graphical genomics viewer (licensed under GPLv2)
  • 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.