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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/hall-lab/bamkit

Software tools for common BAM file manipulations.

Proper citation: bamkit (RRID:SCR_023969) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-PrimerDesigner

Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported.

Proper citation: Bio-PrimerDesigner (RRID:SCR_024082) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/kyrgyzov/lsa_slurm

Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics.

Proper citation: lsa_slurm (RRID:SCR_018134) Copy   

•   Source: SciCrunch Registry

https://github.com/Pithikos/C-Thread-Pool

Software for minimal but powerful thread pool in ANSI C.

Proper citation: C Thread Pool (RRID:SCR_023999) Copy   

•   Source: SciCrunch Registry

https://github.com/smirarab/sepp/

Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.

Proper citation: sepp (RRID:SCR_024327) Copy   

•   Source: SciCrunch Registry

https://www.teuniz.net/edflib/

Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.

Proper citation: EDFlib (RRID:SCR_024010) Copy   

•   Source: SciCrunch Registry

http://www.dclunie.com/dicom3tools.html

Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.

Proper citation: Dicom3tools (RRID:SCR_024008) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/AxPcoords.dist

Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.

Proper citation: AxPcoords (RRID:SCR_023971) Copy   

•   Source: SciCrunch Registry

http://sco.h-its.org/exelixis/web/software/AxParafit/index.html

Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.

Proper citation: AxParafit (RRID:SCR_023968) Copy   

•   Source: SciCrunch Registry

https://github.com/nextstrain/auspice

Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.

Proper citation: Auspice (RRID:SCR_023966) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/assembly-stats

Software to get assembly statistics from FASTA and FASTQ files.

Proper citation: assembly-stats (RRID:SCR_023963) Copy   

•   Source: SciCrunch Registry

https://github.com/thegenemyers/DEXTRACTOR

Software as Bax file decoder and data compressor.

Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy   

•   Source: SciCrunch Registry

https://github.com/nexml/nexml.java

Software repository contains java code for NeXML processing.

Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy   

•   Source: SciCrunch Registry

http://segway.hoffmanlab.org/

The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy   

•   Source: SciCrunch Registry

http://cudasw.sourceforge.net/

CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher

Proper citation: CUDASW++ (RRID:SCR_008862) Copy   

•   Source: SciCrunch Registry