BC Cancer Canada's Michael Smith Genome Sciences Centre

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116 repositories

btllib
Public
Bioinformatics Technology Lab common code library
python library bioinformatics algorithms genome bloom-filter data-structures cpp
C++
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Other
•5•23•24•5•Updated Nov 6, 2024Nov 6, 2024
arcs
Public
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
science c-plus-plus genome graph assembler scaffold oxford-nanopore 10xgenomics pacbio-data nanopore-sequencing
C++
•
GNU General Public License v3.0
•16•91•0•0•Updated Nov 6, 2024Nov 6, 2024
pori_python
Public
Python
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GNU General Public License v3.0
•1•0•1•1•Updated Nov 5, 2024Nov 5, 2024
pori_ipr_client
Public
Integrated Pipeline Reports (IPR) client. The web interface for the reporting application as part of PORI
bioinformatics genomics personalized-medicine pori
TypeScript
•
GNU General Public License v3.0
•1•8•0•3•Updated Nov 5, 2024Nov 5, 2024
NanoSim
Public
Nanopore sequence read simulator
simulator genome oxford-nanopore nanopore-sequencing transcriptome
Python
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Other
•57•242•30•2•Updated Nov 5, 2024Nov 5, 2024
amnatate
Public
Draft genome completeness assessment using hash based approach
C++
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GNU General Public License v3.0
•0•1•0•1•Updated Nov 5, 2024Nov 5, 2024
pori_ipr_api
Public
Integrated Pipeline Reports (IPR) API, the reporting API as part of the PORI platform
bioinformatics genomics personalized-medicine pori
JavaScript
•0•8•0•3•Updated Nov 5, 2024Nov 5, 2024
ntStat
Public
ntStat: a toolkit for statistical analysis of k-mer frequency and depth
C++
•
GNU General Public License v3.0
•0•0•0•0•Updated Nov 3, 2024Nov 3, 2024
goldrush
Public
Linear-time de novo Long Read Assembler
genome-assembly bioinformatics-tool long-read-sequencing bioinformatics
C++
•
GNU General Public License v3.0
•2•35•6•1•Updated Nov 1, 2024Nov 1, 2024
ntEdit
Public
✏️ Genome assembly polishing & SNV detection
c-plus-plus bloom-filter polishing draft-genome variant-detection
C++
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GNU General Public License v3.0
•9•64•0•0•Updated Oct 31, 2024Oct 31, 2024
ntSynt
Public
Detecting multi-genome synteny using minimizer graph mapping
Python
•
GNU General Public License v3.0
•1•70•1•0•Updated Oct 30, 2024Oct 30, 2024
btl
Public
🔬 Bioinformatics Technology Lab, Genome Sciences Centre
HTML
•3•1•4•0•Updated Oct 30, 2024Oct 30, 2024
AMPd-Up
Public
De novo antimicrobial peptide sequence generation with recurrent neural networks
Python
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Other
•0•1•0•0•Updated Oct 30, 2024Oct 30, 2024
biobloom
Public
Create Bloom filters for a given reference and then use it to categorize sequences
C++
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GNU General Public License v3.0
•15•75•9•1•Updated Oct 29, 2024Oct 29, 2024
pori_graphkb_loader
Public
The Loaders for GraphKB. Imports content from external sources via the GraphKB REST API
etl pori
JavaScript
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GNU General Public License v3.0
•4•6•12•2•Updated Oct 23, 2024Oct 23, 2024
tr_catalog
Public
Tandem repeat catalog from public long-read sequence assemblies
Python
•0•1•0•0•Updated Oct 23, 2024Oct 23, 2024
mtGrasp
Public
mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
Python
•
GNU General Public License v3.0
•2•12•1•0•Updated Oct 21, 2024Oct 21, 2024
abyss
Public
🔬 Assemble large genomes using short reads
science bioinformatics genome openmp mpi c-plus-plus bloom-filter assembler scaffold
C++
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Other
•108•311•4•0•Updated Oct 18, 2024Oct 18, 2024
AMPlify
Public
Attentive deep learning model for antimicrobial peptide prediction
Python
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Other
•9•39•2•0•Updated Oct 17, 2024Oct 17, 2024
ntLink
Public
Minimizer-based assembly scaffolding and mapping using long reads
assembly scaffolding long-reads minimizers bioinformatics
Python
•
GNU General Public License v3.0
•7•31•0•1•Updated Oct 11, 2024Oct 11, 2024
ntRoot
Public
🌳 Human ancestry inference from genomic data
genome ancestry snv genome-assembly genomic-data-analysis ancestrydna genomic-data ancestry-inference sequencing-data snv-call
Python
•
GNU General Public License v3.0
•0•4•0•0•Updated Oct 11, 2024Oct 11, 2024
ntJoin
Public
🔗Genome assembly scaffolder using minimizer graphs
Python
•
GNU General Public License v3.0
•15•82•0•0•Updated Oct 2, 2024Oct 2, 2024
goldpolish
Public
GoldPolish (aka GoldRush-Edit) is a long read sequence polisher used in the GoldRush assembler
C++
•
GNU General Public License v3.0
•0•5•1•0•Updated Oct 1, 2024Oct 1, 2024
straglr
Public
Tandem repeat expansion detection or genotyping from long-read alignments
tandem-repeats long-reads bioinformatics genomics
Python
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Other
•8•67•13•0•Updated Sep 26, 2024Sep 26, 2024
MAP
Public
📍Microdilution Assay Processor
microbiology 96-well-plate antimicrobial cytotoxicity plate-reader antimicrobial-susecptibility hemolysis
Python
•0•0•0•0•Updated Sep 20, 2024Sep 20, 2024
pori_graphkb_client
Public
Front-end web client for the GraphKB project
graphdb knowledge-base genomic personalized-medicine pori
TypeScript
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GNU General Public License v3.0
•1•9•14•0•Updated Sep 18, 2024Sep 18, 2024
pori_graphkb_schema
Public
Shared package between the API and GUI for GraphKB which holds the schema definitions and schema-related functions
genomics graphdb knowledge-base personalized-medicine pori
TypeScript
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GNU General Public License v3.0
•0•4•1•0•Updated Sep 6, 2024Sep 6, 2024
long_read_pog
Public
Analysis code for a cohort of Nanopore-sequenced tumours.
HTML
•
MIT License
•0•2•0•1•Updated Sep 5, 2024Sep 5, 2024
tAMPer
Public
tAMPer: antimicrobial peptides toxicity prediction
Jupyter Notebook
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GNU General Public License v3.0
•2•7•1•0•Updated Aug 2, 2024Aug 2, 2024
pori_graphkb_api
Public
REST API for the GraphKB project
genomics graphdb knowledge-base personalized-medicine pori
JavaScript
•
GNU General Public License v3.0
•1•4•6•0•Updated Jul 31, 2024Jul 31, 2024