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https://github.com/reedacartwright/ngila
Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties.
Proper citation: Ngila (RRID:SCR_024133) Copy
https://github.com/medvedevgroup/varmatch
Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes
Proper citation: VarMatch (RRID:SCR_024375) Copy
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
https://github.com/nextflow-io/nextflow
Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.
Proper citation: Nextflow (RRID:SCR_024135) Copy
https://github.com/fccoelho/epigrass
Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.
Proper citation: Epigrass (RRID:SCR_024016) Copy
https://github.com/jnktsj/DNApi/
Software de novo adapter prediction algorithm for small RNA sequencing data.
Proper citation: DNApi (RRID:SCR_024009) Copy
https://www.teuniz.net/edfbrowser/
Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc.
Proper citation: EDFbrowser (RRID:SCR_024021) Copy
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
Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.
Proper citation: Assemblytics (RRID:SCR_023967) Copy
https://zhanggroup.org/NW-align/
Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.
Proper citation: NW-align (RRID:SCR_024138) Copy
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
https://sourceforge.net/projects/surankco/
Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.
Proper citation: surankco (RRID:SCR_024355) Copy
https://pyscanfcs.readthedocs.io/en/stable/
Software application for perpendicular line scanning fluorescence correlation spectroscopy.
Proper citation: pyscanfcs (RRID:SCR_024190) Copy
https://github.com/pyranges/pyranges
Software application for efficient comparison of genomic intervals in Python.
Proper citation: pyranges (RRID:SCR_024191) Copy
https://lcb.infotech.monash.edu/mustang/
Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures.
Proper citation: Mustang (RRID:SCR_024126) Copy
https://zhanglab.ccmb.med.umich.edu/TM-align/
Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons.
Proper citation: TM-align (RRID:SCR_024390) Copy
https://github.com/nawrockie/vadr
Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families.
Proper citation: VADR (RRID:SCR_024377) Copy
http://labs.bio.unc.edu/Vision/FISH/
Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps.
Proper citation: FISH (RRID:SCR_024378) Copy
https://github.com/cbrueffer/tophat-recondition
Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat.
Proper citation: TopHat-Recondition (RRID:SCR_024383) Copy
https://github.com/nanoporetech/tombo
Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal.
Proper citation: Tombo (RRID:SCR_024388) Copy
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