Birol Lab

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92 repositories

pavfinder
Public
:mag: Post Assembly Variants Finder
bioinformatics rna-seq assembly
bioinformatics rna-seq assembly structural-variants gene-fusions splice-variants
Python
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Other
•5•18•1•0•Updated Mar 21, 2026Mar 21, 2026
btl
Public
:microscope: Bioinformatics Technology Lab, Genome Sciences Centre
HTML
•3•2•4•0•Updated Mar 20, 2026Mar 20, 2026
aakomp
Public
Draft genome completeness assessment using k-mer hash based approach
C++
•
GNU General Public License v3.0
•0•2•0•0•Updated Mar 20, 2026Mar 20, 2026
Stash
Public
This repository contains the implementation for the Stash data structure
C++
•
GNU General Public License v3.0
•2•4•0•0•Updated Mar 19, 2026Mar 19, 2026
ntSynt-viz
Public
Multi-genome synteny block visualization tool
Python
•
GNU General Public License v3.0
•4•55•1•0•Updated Mar 19, 2026Mar 19, 2026
goldrush
Public
Linear-time de novo Long Read Assembler
bioinformatics genome-assembly bioinformatics-tool
bioinformatics genome-assembly bioinformatics-tool long-read-sequencing
C++
•
GNU General Public License v3.0
•2•41•4•0•Updated Mar 19, 2026Mar 19, 2026
btllib
Public
📚Bioinformatics Technology Lab common code library
python library bioinformatics
python library bioinformatics algorithms genome cpp bloom-filter data-structures
C++
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Other
•7•28•26•8•Updated Mar 18, 2026Mar 18, 2026
ntSynt
Public
Detecting multi-genome synteny using minimizer graph mapping
Python
•
GNU General Public License v3.0
•2•104•0•0•Updated Mar 18, 2026Mar 18, 2026
physlr
Public
:chains: Construct a Physical Map from Linked Reads
bioinformatics genome-assembly genome-scaffolding
bioinformatics genome-assembly genome-scaffolding 10xgenomics linked-reads bioinformatics-tool
Python
•
GNU General Public License v3.0
•7•18•5•0•Updated Mar 18, 2026Mar 18, 2026
pavfinder_transcriptome
Public
Python
•0•0•1•1•Updated Mar 17, 2026Mar 17, 2026
AMPd-Up
Public
De novo antimicrobial peptide sequence generation with recurrent neural networks
Python
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Other
•0•4•1•0•Updated Mar 17, 2026Mar 17, 2026
AMPlify
Public
Attentive deep learning model for antimicrobial peptide prediction
Python
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Other
•13•56•4•0•Updated Mar 17, 2026Mar 17, 2026
LINKS
Public
⛓ Long Interval Nucleotide K-mer Scaffolder
bloom-filter scaffold long-reads
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•73•0•0•Updated Mar 13, 2026Mar 13, 2026
RNA-Bloom
Public
:hibiscus: reference-free transcriptome assembly for short and long reads
rna-seq denovo-assembly single-cell-rna-seq
rna-seq denovo-assembly single-cell-rna-seq bioinformatics-tool nanopore-sequencing bulk-rna-seq pacbio-sequencing
Java
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Other
•9•108•9•1•Updated Mar 13, 2026Mar 13, 2026
rAMPage
Public
rAMPage: Rapid AMP Annotation and Gene Estimation
Shell
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GNU General Public License v3.0
•1•7•0•0•Updated Mar 13, 2026Mar 13, 2026
ntHash
Public
Fast hash function for DNA/RNA sequences
bioinformatics genomics bloom-filter
bioinformatics genomics bloom-filter hash hash-algorithm hash-methods k-mer-hashing
C++
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MIT License
•15•106•2•3•Updated Mar 13, 2026Mar 13, 2026
ntCard
Public
Estimating k-mer coverage histogram of genomics data
hyperloglog cardinality-estimation k-mer-counting
hyperloglog cardinality-estimation k-mer-counting k-mer-frequency streaming-algorithms
C++
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MIT License
•9•77•9•2•Updated Mar 13, 2026Mar 13, 2026
ntEmbd
Public
Deep learning embedding for nucleotide sequences
Python
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Other
•2•20•3•0•Updated Mar 12, 2026Mar 12, 2026
NanoSim
Public
Nanopore sequence read simulator
simulator genome transcriptome
simulator genome transcriptome oxford-nanopore nanopore-sequencing
Python
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Other
•64•294•35•2•Updated Mar 12, 2026Mar 12, 2026
AMPSeek
Public
Antimicrobial property, protein structure and toxicity detection from peptide sequences
Python
•0•1•0•0•Updated Mar 12, 2026Mar 12, 2026
abyss
Public
:microscope: Assemble large genomes using short reads
science c-plus-plus bioinformatics
science c-plus-plus bioinformatics genome bloom-filter assembler scaffold openmp mpi
C++
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Other
•111•328•5•0•Updated Mar 11, 2026Mar 11, 2026
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•8•2•0•Updated Mar 11, 2026Mar 11, 2026
ABySS-explorer
Public
Visualize genome sequence assemblies
visualization assembly-graph genome-assembly
visualization assembly-graph genome-assembly
Java
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GNU General Public License v3.0
•0•6•0•0•Updated Mar 11, 2026Mar 11, 2026
triAMPh
Public
TaRget Identification of AntiMicrobial Peptides with Heterogeneous graph attention networks
Python
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MIT License
•0•1•0•0•Updated Mar 11, 2026Mar 11, 2026
RAILS
Public
🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling
Perl
•
GNU General Public License v3.0
•5•27•0•0•Updated Mar 10, 2026Mar 10, 2026
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 Mar 10, 2026Mar 10, 2026
PASS
Public
Proteome Assembler with Short peptide Sequence
Perl
•
GNU General Public License v3.0
•2•9•0•0•Updated Mar 10, 2026Mar 10, 2026
ntRoot
Public
🌳 Scalable ancestry from genomic data
genome ancestry snv
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•12•0•0•Updated Mar 10, 2026Mar 10, 2026
SSAKE
Public
🍶 Genome assembly with short sequence reads
dna-sequences genome-scaffolding short-reads
dna-sequences genome-scaffolding short-reads sequence-assembly genome-assembler read-pairs
Perl
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GNU General Public License v2.0
•11•25•1•0•Updated Mar 10, 2026Mar 10, 2026
ntEdit
Public
✏️ Genome assembly polishing & SNV detection
c-plus-plus bloom-filter polishing
c-plus-plus bloom-filter polishing draft-genome variant-detection
C++
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GNU General Public License v3.0
•10•73•0•1•Updated Mar 10, 2026Mar 10, 2026