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https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
Software library as set of classes for creating statistical genetic programs.
Proper citation: libStatGen (RRID:SCR_024093) Copy
https://github.com/rvaser/thread_pool
Software C++ thread pool library.
Proper citation: ThreadPool (RRID:SCR_024094) Copy
https://github.com/rizkg/BBHash
Software library for building minimal perfect hash function. Designed to handle large scale datasets.
Proper citation: BBHash (RRID:SCR_023972) Copy
https://github.com/jdidion/atropos
Software tool for specific, sensitive, and speedy trimming of NGS reads.
Proper citation: Atropos (RRID:SCR_023962) Copy
https://github.com/y-256/libdivsufsort
Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.
Proper citation: libdivsufsort (RRID:SCR_024079) Copy
http://libdisorder.freshdefense.net/
Software C library for entropy measurement of byte streams and other data.
Proper citation: libdisorder (RRID:SCR_024072) Copy
https://github.com/BIC-MNI/libminc
Software core library and API of the Medical Image NetCDF toolkit.
Proper citation: libminc (RRID:SCR_024086) Copy
https://github.com/kdm9/libqcpp
Software C++11 library for next-gen sequence quality control and assessment.
Proper citation: libqc++ (RRID:SCR_024088) Copy
https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages.
Proper citation: SSW Library (RRID:SCR_024089) Copy
https://svi-opensource.github.io/libics/
Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing.
Proper citation: libics (RRID:SCR_024085) Copy
https://sourceforge.net/projects/placnet/
Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.
Proper citation: Placnet (RRID:SCR_024176) Copy
https://prinseq.sourceforge.net/
Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.
Proper citation: PRINSEQ (RRID:SCR_024178) Copy
https://sourceforge.net/projects/poamsa/
Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.
Proper citation: POA (RRID:SCR_024172) Copy
https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.
Proper citation: PLIP (RRID:SCR_024173) Copy
https://github.com/COMBINE-lab/RapMap
Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping
Proper citation: rapmap (RRID:SCR_024204) Copy
https://github.com/silx-kit/pyFAI
Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.
Proper citation: pyFAI (RRID:SCR_024186) Copy
https://github.com/rvalieris/parallel-fastq-dump
Software wrapper to speed up downloading process by dividing the work into multiple threads.
Proper citation: parallel-fastq-dump (RRID:SCR_024150) Copy
https://github.com/FlorianThibord/OptimiR
Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.
Proper citation: OptimiR (RRID:SCR_024149) Copy
https://github.com/FePhyFoFum/phyx
Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.
Proper citation: Phyx (RRID:SCR_024164) Copy
https://qtltools.github.io/qtltools/
Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps.
Proper citation: qtltools (RRID:SCR_024200) Copy
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