BC Cancer Canada's Michael Smith Genome Sciences Centre

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117 repositories

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•1•Updated Mar 12, 2025Mar 12, 2025
unikseq
Public
🧬 Unique (& conserved) DNA sequence identification
Perl
•
GNU General Public License v3.0
•1•11•0•0•Updated Mar 12, 2025Mar 12, 2025
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•5•Updated Mar 12, 2025Mar 12, 2025
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 Mar 12, 2025Mar 12, 2025
pori_python
Public
Python
•
GNU General Public License v3.0
•1•0•1•2•Updated Mar 10, 2025Mar 10, 2025
btl
Public
🔬 Bioinformatics Technology Lab, Genome Sciences Centre
HTML
•3•1•4•0•Updated Mar 8, 2025Mar 8, 2025
pori_graphkb_loader
Public
The Loaders for GraphKB. Imports content from external sources via the GraphKB REST API
etl pori
JavaScript
•
GNU General Public License v3.0
•4•6•12•2•Updated Mar 5, 2025Mar 5, 2025
NanoSim
Public
Nanopore sequence read simulator
simulator genome oxford-nanopore nanopore-sequencing transcriptome
Python
•
Other
•59•261•32•2•Updated Mar 2, 2025Mar 2, 2025
pori_graphkb_client
Public
Front-end web client for the GraphKB project
graphdb knowledge-base genomic personalized-medicine pori
TypeScript
•
GNU General Public License v3.0
•1•9•14•0•Updated Feb 25, 2025Feb 25, 2025
ntEdit
Public
✏️ Genome assembly polishing & SNV detection
c-plus-plus bloom-filter polishing draft-genome variant-detection
C++
•
GNU General Public License v3.0
•9•66•0•0•Updated Feb 21, 2025Feb 21, 2025
HLAminer
Public
⛏ HLA predictions from NGS shotgun data
alignments oxford-nanopore hla-prediction targeted-assemblies hla-sequence shotgun-sequence-datasets
Perl
•
Other
•15•52•0•0•Updated Feb 18, 2025Feb 18, 2025
tr_catalog
Public
Tandem repeat catalog from public long-read sequence assemblies
Python
•0•1•1•0•Updated Feb 11, 2025Feb 11, 2025
mtGrasp
Public
mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
Python
•
GNU General Public License v3.0
•2•15•2•0•Updated Feb 10, 2025Feb 10, 2025
AMPlify
Public
Attentive deep learning model for antimicrobial peptide prediction
Python
•
Other
•11•41•3•0•Updated Feb 7, 2025Feb 7, 2025
straglr
Public
Tandem repeat expansion detection or genotyping from long-read alignments
tandem-repeats long-reads bioinformatics genomics
Python
•
Other
•10•96•17•0•Updated Feb 7, 2025Feb 7, 2025
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•38•6•0•Updated Jan 29, 2025Jan 29, 2025
btllib
Public
Bioinformatics Technology Lab common code library
python library bioinformatics algorithms genome bloom-filter data-structures cpp
C++
•
Other
•6•25•25•7•Updated Jan 27, 2025Jan 27, 2025
ntSynt-viz
Public
Multi-genome synteny block visualization tool
Python
•
GNU General Public License v3.0
•4•30•1•0•Updated Jan 24, 2025Jan 24, 2025
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 Jan 24, 2025Jan 24, 2025
ntEmbd
Public
Deep learning embedding for nucleotide sequences
Python
•
Other
•3•17•0•0•Updated Jan 21, 2025Jan 21, 2025
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•6•0•0•Updated Jan 20, 2025Jan 20, 2025
ntSynt
Public
Detecting multi-genome synteny using minimizer graph mapping
Python
•
GNU General Public License v3.0
•2•76•1•0•Updated Jan 16, 2025Jan 16, 2025
peekseq
Public
De novo protein-coding potential calculator using a k-mer approach
Perl
•
GNU General Public License v3.0
•0•4•0•0•Updated Dec 27, 2024Dec 27, 2024
tAMPer
Public
tAMPer: antimicrobial peptides toxicity prediction
Jupyter Notebook
•
GNU General Public License v3.0
•2•7•1•0•Updated Dec 4, 2024Dec 4, 2024
amnatate
Public
Draft genome completeness assessment using hash based approach
C++
•
GNU General Public License v3.0
•0•2•0•1•Updated Nov 26, 2024Nov 26, 2024
biobloom
Public
Create Bloom filters for a given reference and then use it to categorize sequences
C++
•
GNU General Public License v3.0
•15•76•9•0•Updated Nov 26, 2024Nov 26, 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•92•1•0•Updated Nov 6, 2024Nov 6, 2024
AMPd-Up
Public
De novo antimicrobial peptide sequence generation with recurrent neural networks
Python
•
Other
•0•1•1•0•Updated Oct 30, 2024Oct 30, 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
•110•316•6•0•Updated Oct 18, 2024Oct 18, 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•37•0•0•Updated Oct 11, 2024Oct 11, 2024