Ex Center for Algorithmic Biotechnology

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30 repositories

IsoQuant
Public
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
bioinformatics rna-seq nanopore ngs pacbio transcriptomics
Python
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Other
•13•153•39•2•Updated Nov 19, 2024Nov 19, 2024
quast-website
Public
Django web interface for Quast assembly assessment tool: https://github.com/ablab/quast
HTML
•2•5•0•0•Updated Nov 14, 2024Nov 14, 2024
quast
Public
Genome assembly evaluation tool
visualization bioinformatics genome-assembly-evaluation contigs
AMPL
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Other
•78•409•72•2•Updated Nov 14, 2024Nov 14, 2024
spades
Public
SPAdes Genome Assembler
sequencing next-generation-sequencing illumina genome-assembly sequence-assembler transcriptome-assembly metagenome-assembly
C++
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Other
•138•761•252•4•Updated Nov 6, 2024Nov 6, 2024
rnaquast
Public
Quality assessment of de novo transcriptome assemblies from RNA-Seq data
transcriptome-assembly quality-evaluation
Python
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Other
•6•19•8•0•Updated Oct 25, 2024Oct 25, 2024
nerpa
Public
C++
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Other
•3•14•0•3•Updated Mar 15, 2024Mar 15, 2024
metarna
Public
Python
•0•0•0•2•Updated Jul 6, 2023Jul 6, 2023
orf-search
Public
ORF search on assembly graphs
Python
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Other
•3•6•0•0•Updated Apr 12, 2023Apr 12, 2023
metaGT
Public
Pipeline for metagenome and metatranscriptome joint assembly
metagenomics metatranscriptomics
Nextflow
•
MIT License
•2•18•2•0•Updated Mar 3, 2023Mar 3, 2023
VerityMap
Public
C++
•
GNU General Public License v3.0
•5•31•9•1•Updated Feb 22, 2023Feb 22, 2023
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.3k•0•0•0•Updated Jan 22, 2023Jan 22, 2023
graphamr
Public
Antibiotic prediction from metagenome assembly graphs
Nextflow
•2•8•3•1•Updated Sep 19, 2022Sep 19, 2022
stringdecomposer
Public
Tool for decomposition centromeric assemblies and long reads into monomers
C++
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Other
•2•34•5•0•Updated Sep 17, 2022Sep 17, 2022
npdtools
Public
Natural Product Discovery tools -- a toolkit containing various pipelines for in silico analysis of natural product mass spectrometry data
bioinformatics metabolomics mass-spectrometry natural-products
9•23•3•0•Updated Aug 19, 2022Aug 19, 2022
quast_snakemake
Public
Python
•0•3•0•0•Updated Jul 29, 2022Jul 29, 2022
NPvis
Public
Interactive visualizer for MS/MS fragmentation of natural products
JavaScript
•0•0•2•0•Updated Jun 21, 2022Jun 21, 2022
HORmon
Public
Python
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Other
•1•8•0•1•Updated May 6, 2022May 6, 2022
platform_comparison
Public
Comparing Platforms
Python
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Other
•1•2•0•0•Updated Feb 2, 2022Feb 2, 2022
holy-build-box
Public
System for building cross-distribution Linux binaries
Shell
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MIT License
•74•0•0•0•Updated Jan 31, 2022Jan 31, 2022
viralComplete
Public
viralComplete: BLAST-based viral completeness verification
Python
•1•23•0•0•Updated Oct 4, 2021Oct 4, 2021
viralVerify
Public
viralVerify: viral contig verification tool
Python
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MIT License
•12•65•4•0•Updated Aug 22, 2021Aug 22, 2021
TandemTools
Public
Tool for assessing/improving assembly quality in extra-long tandem repeats
C++
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Other
•5•45•7•1•Updated Feb 23, 2021Feb 23, 2021
covid19_variation_analysis
Public
Python
•2•1•0•0•Updated Jun 21, 2020Jun 21, 2020
plasmidVerify
Public
plasmidVerify: plasmid contig verification tool
Python
•3•12•1•0•Updated Apr 30, 2020Apr 30, 2020
y-tools
Public
C++
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Other
•2•3•0•1•Updated Jul 26, 2018Jul 26, 2018
basespace_gatk_app
Public
Repo for creating BaseSpace Apps
Python
•0•1•0•0•Updated Dec 27, 2015Dec 27, 2015
rectangles
Public archive
Python
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Other
•0•0•0•0•Updated Dec 20, 2012Dec 20, 2012
external-tools
Public archive
C++
•1•3•0•0•Updated Mar 15, 2012Mar 15, 2012
TagFinder05
Public archive
Java
•1•3•0•0•Updated Mar 6, 2012Mar 6, 2012
TagFinder
Public archive
Java
•1•4•0•0•Updated Mar 6, 2012Mar 6, 2012