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https://github.com/lh3/miniasm

Software OLC-based de novo assembler for noisy long reads.

Proper citation: Miniasm (RRID:SCR_024114) Copy   

•   Source: SciCrunch Registry

https://github.com/cogent3/cogent3

Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.

Proper citation: PyCogent (RRID:SCR_024192) Copy   

•   Source: SciCrunch Registry

http://libdisorder.freshdefense.net/

Software C library for entropy measurement of byte streams and other data.

Proper citation: libdisorder (RRID:SCR_024072) Copy   

•   Source: SciCrunch Registry

https://github.com/open2c/cooler

Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays.

Proper citation: Cooler (RRID:SCR_024194) Copy   

•   Source: SciCrunch Registry

https://github.com/dib-lab/sourmash

Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.

Proper citation: sourmash (RRID:SCR_024347) Copy   

•   Source: SciCrunch Registry

https://micans.org/mcl/

Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs.

Proper citation: MCL (RRID:SCR_024109) Copy   

•   Source: SciCrunch Registry

https://github.com/BIC-MNI/libminc

Software core library and API of the Medical Image NetCDF toolkit.

Proper citation: libminc (RRID:SCR_024086) Copy   

•   Source: SciCrunch Registry

https://github.com/rcsb/mmtf-python

Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.

Proper citation: mmtf-python (RRID:SCR_024120) Copy   

•   Source: SciCrunch Registry

https://github.com/kdm9/libqcpp

Software C++11 library for next-gen sequence quality control and assessment.

Proper citation: libqc++ (RRID:SCR_024088) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages!

Proper citation: Vector Alignment Search Tool (RRID:SCR_010655) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/rki_bioinformatics/IDeFIX

Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s).

Proper citation: IDeFIX (RRID:SCR_024033) Copy   

•   Source: SciCrunch Registry

https://github.com/lbcb-sci/graphmap2

Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices

Proper citation: GraphMap2 (RRID:SCR_024035) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/andreas.andrusch/paipline

Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples.

Proper citation: PAIPline (RRID:SCR_024151) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/kineticsTools

Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol.

Proper citation: kineticsTools (RRID:SCR_024049) Copy   

•   Source: SciCrunch Registry

https://itk.org/

Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Proper citation: Insight Toolkit (RRID:SCR_024040) Copy   

•   Source: SciCrunch Registry

https://github.com/Nextomics/nextsv

Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.

Proper citation: NextSV (RRID:SCR_024134) Copy   

•   Source: SciCrunch Registry

http://www.danielwilson.me.uk/omegaMap.html

Software tool for detecting natural selection and recombination in DNA or RNA sequences.

Proper citation: omegaMap (RRID:SCR_024143) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/microbegps/

Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.

Proper citation: MicrobeGPS (RRID:SCR_024112) Copy   

•   Source: SciCrunch Registry