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    26 repositories

    • EDGE_workflows

      Public
      Perl
      •
      GNU General Public License v3.0
      •1•0•0•2•Updated Dec 18, 2024Dec 18, 2024

    • NASA_GeneLab_workflows

      Public
      WDL
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • scRNA-seq

      Public
      Python
      •0•2•0•0•Updated Oct 14, 2024Oct 14, 2024

    • EDGE

      Public
      EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
      bioinformaticsgenomics
      Perl
      •
      GNU General Public License v3.0
      •33•73•5•0•Updated Sep 30, 2024Sep 30, 2024

    • synthetic_transkingdom_data

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 21, 2024Mar 21, 2024

    • normalCowboy

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 13, 2024Mar 13, 2024

    • PhaME

      Public
      Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
      Perl
      •
      GNU General Public License v3.0
      •18•31•14•1•Updated Nov 28, 2023Nov 28, 2023

    • phame-app

      Public
      JavaScript
      •
      Other
      •0•0•2•8•Updated May 25, 2023May 25, 2023

    • ramifi

      Public
      Recombinant And Mixed-Infection Finder for SARS-CoV-2
      HTML
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Jan 25, 2023Jan 25, 2023

    • nmdc-schema

      Public
      This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
      Python
      •
      Creative Commons Zero v1.0 Universal
      •8•0•0•0•Updated Feb 11, 2022Feb 11, 2022

    • Lo-et-al-Bioinformatics-EC-19-data

      Public
      0•0•0•0•Updated Jan 14, 2022Jan 14, 2022

    • assay_validation

      Public
      This is a web-app and workflow for computationally screening PCR-based assays
      Python
      •
      GNU General Public License v3.0
      •1•4•1•0•Updated Nov 1, 2021Nov 1, 2021

    • KWAGE

      Public
      Ultra-fast, Bloom filter-based sequence search
      C++
      •
      Other
      •2•6•0•1•Updated Jun 23, 2021Jun 23, 2021

    • kbase-gottcha2

      Public
      GOTTCHA2 KBase app
      Python
      •
      MIT License
      •2•0•1•0•Updated May 26, 2021May 26, 2021

    • DETEQT

      Public
      Diagnostic targeted sequencing adjudication
      Perl
      •
      Other
      •1•0•0•0•Updated Apr 26, 2021Apr 26, 2021

    • PCRamp

      Public
      Software for designing multiplex-compatible, PCR-based enrichment assays
      C++
      •
      Other
      •0•5•1•0•Updated Jan 26, 2021Jan 26, 2021

    • kbase-metaphlan2

      Public
      KBase wrapper for MetaPhAn2
      Python
      •
      MIT License
      •0•0•0•1•Updated Nov 25, 2020Nov 25, 2020

    • piret

      Public
      Pythonic PiReT
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated Oct 21, 2020Oct 21, 2020

    • gottcha2-custom-db

      Public
      Generates custom GOTTCHA2 database from a set of genomes
      0•0•0•0•Updated Aug 31, 2020Aug 31, 2020

    • FaQCs

      Public
      Quality Control of Next Generation Sequencing Data
      C++
      •
      GNU General Public License v3.0
      •11•22•1•0•Updated Aug 18, 2020Aug 18, 2020

    • metamer

      Public
      Cluster shotgun sequencing samples
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 7, 2019Oct 7, 2019

    • PanGIA

      Public
      Python
      •
      Other
      •2•7•9•0•Updated Aug 16, 2019Aug 16, 2019

    • GOTTCHA

      Public
      Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Please visit our homepage:
      Perl
      •
      GNU General Public License v3.0
      •10•23•13•0•Updated Jan 29, 2019Jan 29, 2019

    • rMoore

      Public
      Moore genome citation tracker
      R
      •1•0•0•0•Updated Nov 22, 2017Nov 22, 2017

    • MeGAMerge

      Public
      MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
      Perl
      •
      Other
      •7•14•6•0•Updated Dec 7, 2016Dec 7, 2016

    • ADEPT

      Public
      ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution for the dataset being analyzed.
      Perl
      •
      GNU General Public License v3.0
      •4•7•0•0•Updated Jan 5, 2016Jan 5, 2016