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https://github.com/andersen-lab/ivar
Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Proper citation: iVar (RRID:SCR_024045) Copy
https://changeo.readthedocs.io
Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences.
Proper citation: Change-O (RRID:SCR_023986) Copy
Open Source software modular Java libraries for cheminformatics.
Proper citation: CDK (RRID:SCR_023985) Copy
https://github.com/gramos/imagetooth
Software library to generate images for odontograms.Allows to choose between png or jpg images.
Proper citation: ImageTooth (RRID:SCR_024039) Copy
https://github.com/rdpstaff/TaxonomyTree
Software library used by other RDP tools.TaxonomyTree building and traversal utility classes.
Proper citation: TaxonomyTree (RRID:SCR_024090) Copy
https://metacpan.org/dist/Sort-Key-Top
Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.
Proper citation: Sort-Key-Top (RRID:SCR_024092) Copy
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://opencfu.sourceforge.net/
Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit.
Proper citation: OpenCFU (RRID:SCR_024142) Copy
https://github.com/GATB/gatb-core
Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis.
Proper citation: GATB (RRID:SCR_024024) 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/gt1/bambamc
Software package contains lightweight C implementation of name collating BAM file input and BAM file output.
Proper citation: bambamc (RRID:SCR_023970) Copy
Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard.
Proper citation: Odil (RRID:SCR_024140) Copy
https://github.com/hall-lab/bamkit
Software tools for common BAM file manipulations.
Proper citation: bamkit (RRID:SCR_023969) 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
https://github.com/lh3/miniasm
Software OLC-based de novo assembler for noisy long reads.
Proper citation: Miniasm (RRID:SCR_024114) 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://metacpan.org/dist/FAST
Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.
Proper citation: FAST Analysis of Sequences Toolbox (RRID:SCR_024074) Copy
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
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