BC Cancer Canada's Michael Smith Genome Sciences Centre

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118 repositories

btl
Public
🔬 Bioinformatics Technology Lab, Genome Sciences Centre
HTML
•3•2•4•0•Updated May 30, 2025May 30, 2025
straglr
Public
Tandem repeat expansion detection or genotyping from long-read alignments
tandem-repeats long-reads bioinformatics genomics
Python
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Other
•10•113•24•0•Updated May 29, 2025May 29, 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•4•Updated May 29, 2025May 29, 2025
aakomp
Public
Draft genome completeness assessment using k-mer hash based approach
C++
•
GNU General Public License v3.0
•0•2•0•1•Updated May 29, 2025May 29, 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
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GNU General Public License v3.0
•1•8•0•2•Updated May 26, 2025May 26, 2025
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•3•Updated May 14, 2025May 14, 2025
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 May 14, 2025May 14, 2025
pori_python
Public
Python
•
GNU General Public License v3.0
•2•0•2•3•Updated May 14, 2025May 14, 2025
btllib
Public
Bioinformatics Technology Lab common code library
python library bioinformatics algorithms genome bloom-filter data-structures cpp
C++
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Other
•6•25•25•8•Updated May 12, 2025May 12, 2025
ntStat
Public
ntStat: a toolkit for statistical analysis of k-mer frequency and depth
C++
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GNU General Public License v3.0
•0•0•0•0•Updated May 7, 2025May 7, 2025
ntSynt
Public
Detecting multi-genome synteny using minimizer graph mapping
Python
•
GNU General Public License v3.0
•2•78•2•0•Updated May 2, 2025May 2, 2025
tr_catalog
Public
Tandem repeat catalog from public long-read sequence assemblies
Python
•0•1•0•0•Updated Apr 17, 2025Apr 17, 2025
AMPd-Up
Public
De novo antimicrobial peptide sequence generation with recurrent neural networks
Python
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Other
•0•3•1•0•Updated Apr 15, 2025Apr 15, 2025
HLAminer
Public
⛏ HLA predictions from NGS shotgun data
alignments oxford-nanopore hla-prediction targeted-assemblies hla-sequence shotgun-sequence-datasets
Perl
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Other
•15•53•0•0•Updated Apr 15, 2025Apr 15, 2025
triAMPh
Public
TaRget Identification of AntiMicrobial Peptides with Heterogenious graph attention networks
Python
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MIT License
•0•1•0•0•Updated Apr 3, 2025Apr 3, 2025
LINKS
Public
⛓ Long Interval Nucleotide K-mer Scaffolder
bloom-filter scaffold long-reads draft-assembly extract-kmer-pairs genome-assemblies scaffold-layout
Perl
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GNU General Public License v3.0
•16•74•0•0•Updated Apr 1, 2025Apr 1, 2025
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•320•4•0•Updated Mar 27, 2025Mar 27, 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 Mar 27, 2025Mar 27, 2025
ntEmbd
Public
Deep learning embedding for nucleotide sequences
Python
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Other
•3•18•2•0•Updated Mar 26, 2025Mar 26, 2025
goldpolish
Public
GoldPolish (aka GoldRush-Edit) is a long read sequence polisher used in the GoldRush assembler
C++
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GNU General Public License v3.0
•0•6•1•0•Updated Mar 24, 2025Mar 24, 2025
AMPlify
Public
Attentive deep learning model for antimicrobial peptide prediction
Python
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Other
•11•48•3•0•Updated Mar 22, 2025Mar 22, 2025
unikseq
Public
🧬 Unique (& conserved) DNA sequence identification
Perl
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GNU General Public License v3.0
•1•12•0•0•Updated Mar 12, 2025Mar 12, 2025
NanoSim
Public
Nanopore sequence read simulator
simulator genome oxford-nanopore nanopore-sequencing transcriptome
Python
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Other
•60•269•33•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
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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++
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GNU General Public License v3.0
•9•68•0•0•Updated Feb 21, 2025Feb 21, 2025
mtGrasp
Public
mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
Python
•
GNU General Public License v3.0
•2•17•4•0•Updated Feb 10, 2025Feb 10, 2025
goldrush
Public
Linear-time de novo Long Read Assembler
genome-assembly bioinformatics-tool long-read-sequencing bioinformatics
C++
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GNU General Public License v3.0
•2•40•7•0•Updated Jan 29, 2025Jan 29, 2025
ntSynt-viz
Public
Multi-genome synteny block visualization tool
Python
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GNU General Public License v3.0
•4•38•1•0•Updated Jan 24, 2025Jan 24, 2025
peekseq
Public
De novo protein-coding potential calculator using a k-mer approach
Perl
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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
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GNU General Public License v3.0
•2•9•1•0•Updated Dec 4, 2024Dec 4, 2024