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http://gowiki.tamu.edu/wiki/

A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase...

Proper citation: GONUTS (RRID:SCR_000653) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dkessner/forqs

Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits.

Proper citation: forqs (RRID:SCR_000643) Copy   

•   Source: SciCrunch Registry

Discontinued

https://github.com/PacificBiosciences/blasr

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLASR (RRID:SCR_000764) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmcloser/

Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

Proper citation: GMcloser (RRID:SCR_000646) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/detecttd/

Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.

Proper citation: detecttd (RRID:SCR_000681) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fastuniq/

A software tool for removal of de novo duplicates in paired short DNA sequences.

Proper citation: FastUniq (RRID:SCR_000682) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4474950

A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.

Proper citation: Sequencing Analysis Software (RRID:SCR_000718) Copy   

•   Source: SciCrunch Registry

https://github.com/shinout/clipcrop

Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.

Proper citation: clipcrop (RRID:SCR_000678) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/triagetools/

A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.

Proper citation: TriageTools (RRID:SCR_000675) Copy   

•   Source: SciCrunch Registry

http://software.markdpreston.com/varb

A variation browsing and analysis tool for variants derived from next-generation sequencing data.

Proper citation: VarB (RRID:SCR_000671) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/bamseek/

A Large File Viewer for BAM and SAM alignment files.

Proper citation: BAMseek (RRID:SCR_000672) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-toolbox/

A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.

Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/operasf/

A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

Proper citation: Opera (RRID:SCR_000665) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/esb/PiNGO/

A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: PiNGO (RRID:SCR_000692) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/rmap/

Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.

Proper citation: RMAP (RRID:SCR_000695) Copy   

•   Source: SciCrunch Registry

https://github.com/iontorrent/TMAP

Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

Proper citation: TMAP (RRID:SCR_000687) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/glycoworkbench/

A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.

Proper citation: GlycoWorkbench (RRID:SCR_000782) Copy   

•   Source: SciCrunch Registry

http://www.brown.edu/Research/Istrail_Lab/hapcompass.php

Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings.

Proper citation: HapCompass (RRID:SCR_000942) Copy   

•   Source: SciCrunch Registry

https://github.com/akiomiyao/tif

A search program to detect insertions of transposable element from short reads of next generation sequencer.

Proper citation: Transposon Insertion Finder (RRID:SCR_001159) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

R package with tools for analyzing and visualizing bisulfite sequencing data.

Proper citation: bsseq (RRID:SCR_001072) Copy   

•   Source: SciCrunch Registry