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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://paleogenomics.irmacs.sfu.ca/FPSAC/
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
Proper citation: FPSAC (RRID:SCR_000555) Copy
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
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
http://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
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
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
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
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
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
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
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
http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html
Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Proper citation: ADaCGH2 (RRID:SCR_001981) Copy
http://cran.r-project.org/web/packages/PurBayes/
An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
Proper citation: PurBayes (RRID:SCR_002068) Copy
https://github.com/BEETL/BEETL
Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.
Proper citation: BEETL-fastq (RRID:SCR_002341) Copy
Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra.
Proper citation: pymzML (RRID:SCR_002500) Copy
http://pfind.ict.ac.cn/software/pLink/index.html
Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Proper citation: pFind Studio: pLink (RRID:SCR_000084) Copy
https://code.google.com/p/guardd/
MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.
Proper citation: GUARDD (RRID:SCR_000040) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html
Software that establishes a bridge between GEO and BioConductor.
Proper citation: GEOquery (RRID:SCR_000146) Copy
http://sourceforge.net/projects/gemsim/
A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.
Proper citation: GemSIM (RRID:SCR_000167) Copy
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