Quadram Institute Bioscience

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99 repositories

ARG-Snipper
Public
Benchmarking of AMR detection tools using shot-gun metagenomic datasets
0•0•0•0•Updated Nov 29, 2024Nov 29, 2024
binfie-notes
Public
Bioinformatics notes
JavaScript
•
MIT License
•1.5k•0•0•0•Updated Nov 29, 2024Nov 29, 2024
mc-spike
Public
R
•
GNU General Public License v3.0
•1•0•0•0•Updated Nov 27, 2024Nov 27, 2024
cloudgene3
Public
A framework to build Software As A Service (SaaS) platforms for Nextflow pipelines.
Java
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MIT License
•2•0•0•0•Updated Nov 22, 2024Nov 22, 2024
n50
Public
Calculate N50 from FASTA and FASTX files
C
•
MIT License
•0•0•0•0•Updated Nov 21, 2024Nov 21, 2024
QuaTradis
Public
A pipeline to analyse transposon directed insertion-site sequencing
Gnuplot
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GNU General Public License v3.0
•0•3•2•0•Updated Nov 19, 2024Nov 19, 2024
st_illumina_sample_sheet_validator
Public
Sample sheet validator for demultiplexing Illumina runs
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Nov 7, 2024Nov 7, 2024
sample_sheet_validator
Public
Python script validates the contents of a Nextseq 2k sample sheet, ensuring that it meets the expected format
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Nov 7, 2024Nov 7, 2024
qib-irida-uploader
Public
A wrapper of iridauploader for creating project and uploading samples to QIB IRIDA
Python
•1•0•0•0•Updated Oct 25, 2024Oct 25, 2024
ebame-viromics
Public
Ebame workshop website, built by P2PU
SCSS
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MIT License
•496•0•0•0•Updated Oct 20, 2024Oct 20, 2024
phylobarcode
Public
<pilot> in-silico amplicons optimised for phylogenetic signal
phylogenetics metabarcoding amplicon primers
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Oct 18, 2024Oct 18, 2024
mg-tk
Public
metagenomic toolkit - end-to-end solution for analysing metagenomes
Perl
•
GNU General Public License v2.0
•2•1•0•0•Updated Oct 9, 2024Oct 9, 2024
NBI-Slurm
Public
Experimental interface to slurm
perl
Perl
•0•1•0•0•Updated Sep 25, 2024Sep 25, 2024
uvaia
Public
Reference-based alignment and sequence database search of SARS-CoV-2 genomes.
genomics nearest-neighbor-search alignment search-algorithm viral-genomics sars-cov-2 bioinformatics
C
•
GNU General Public License v3.0
•0•4•0•0•Updated Sep 2, 2024Sep 2, 2024
peroba
Public
Phylogenetic Epidemiology with ROBust Assignment
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 19, 2024Aug 19, 2024
biomcmc-lib
Public
C library with lowlevel functions used by other software
C
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 19, 2024Aug 19, 2024
tatajuba
Public
Identification and classification of homopolymeric tracts from reads.
genomics phylogenetics variant-analysis bioinformatics
C
•
GNU General Public License v3.0
•0•5•2•0•Updated Aug 19, 2024Aug 19, 2024
amburana
Public
Alignment-free sequence clustering
C
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 19, 2024Aug 19, 2024
biobakery-2024
Public
A QIB Workshop on popular tools part of the "BioBakery" suite (https://github.com/biobakery/biobakery)
HTML
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Aug 13, 2024Aug 13, 2024
tweety-gut
Public
Metagenomic investigation of the faecal microbiomes of great tits and blue tits provides insights into the host, diet, pathogens and microbial biodiversity
GNU General Public License v3.0
•0•0•0•0•Updated Aug 7, 2024Aug 7, 2024
2024-campymags
Public
Datasets and scripts for article "Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool"
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Jul 30, 2024Jul 30, 2024
qib-jira
Public
Fetching records from QIB Cloud Jira to a local database
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 9, 2024Jul 9, 2024
uflow
Public
USEARCH based workflow
Python
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Apache License 2.0
•0•0•0•0•Updated Jul 8, 2024Jul 8, 2024
q2-usearch
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jul 2, 2024Jul 2, 2024
template_qib_report
Public
Template of a (PDF/HTML) report document using pandoc
CSS
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GNU General Public License v3.0
•0•1•0•0•Updated Jun 21, 2024Jun 21, 2024
datasciencegroup
Public
Scripts and docs from the datascienceatqib group
Jupyter Notebook
•
GNU General Public License v3.0
•0•4•0•0•Updated Jun 21, 2024Jun 21, 2024
galaxy-front-page
Public
galaxy-front-page
SCSS
•0•0•0•0•Updated Jun 17, 2024Jun 17, 2024
workshops-2024
Public
Core Bioinformatics Workshops at the Quadram Institute Bioscience
Jupyter Notebook
•
MIT License
•916•0•0•0•Updated Jun 7, 2024Jun 7, 2024
galaxy-tools
Public
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
bioinformatics nanopore pacbio amr mlst galaxy plasmid long-read-sequencing biotradis
HTML
•3•4•0•0•Updated Jun 4, 2024Jun 4, 2024
q2-vsearch
Public
vsearch plugin for QIIME 2
Python
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BSD 3-Clause "New" or "Revised" License
•20•0•0•0•Updated Jun 3, 2024Jun 3, 2024