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http://mfuzz.sysbiolab.eu/

Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

Proper citation: Mfuzz (RRID:SCR_000523) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/pindel/0.2.4/

Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

Proper citation: Pindel (RRID:SCR_000560) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/genome_bio/siphy/

Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

Proper citation: SiPhy (RRID:SCR_000564) Copy   

•   Source: SciCrunch Registry

http://lilab.stanford.edu/SNPiR/

Software for reliable Identification of Genomic Variants Using RNA-seq Data.

Proper citation: SNPiR (RRID:SCR_000557) Copy   

•   Source: SciCrunch Registry

http://paleogenomics.irmacs.sfu.ca/FPSAC/

Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

Proper citation: FPSAC (RRID:SCR_000555) Copy   

•   Source: SciCrunch Registry

https://posit.co/

Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).

Proper citation: RStudio (RRID:SCR_000432) Copy   

•   Source: SciCrunch Registry

http://drfast.sourceforge.net/

A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.

Proper citation: drFAST (RRID:SCR_000586) Copy   

•   Source: SciCrunch Registry

http://genome.crg.es/software/gfftools/GFF2PS.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.

Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy   

•   Source: SciCrunch Registry

http://bioinfo2.ugr.es/NGSmethPipe/

A software tool which generates high-quality methylation maps.

Proper citation: NGSmethPipe (RRID:SCR_000583) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/~cpatton/maxc.html

A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration.

Proper citation: MAXCHELATOR (RRID:SCR_000459) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/neo/

A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.

Proper citation: Neo (RRID:SCR_000634) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/contest

A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

Proper citation: ContEst (RRID:SCR_000595) 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.

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/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

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://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