All

92 repositories

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 27, 2026Mar 27, 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++
•
Other
•111•329•5•0•Updated Mar 27, 2026Mar 27, 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
•
GNU General Public License v3.0
•16•73•0•0•Updated Mar 27, 2026Mar 27, 2026
arcs
Public
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
science c-plus-plus bioinformatics
science c-plus-plus bioinformatics genome graph assembler scaffold oxford-nanopore 10xgenomics pacbio-data
C++
•
GNU General Public License v3.0
•14•95•0•0•Updated Mar 27, 2026Mar 27, 2026
HLAminer
Public
⛏ HLA predictions from NGS shotgun data
alignments oxford-nanopore hla-prediction
alignments oxford-nanopore hla-prediction targeted-assemblies hla-sequence shotgun-sequence-datasets
Perl
•
Other
•15•55•0•0•Updated Mar 27, 2026Mar 27, 2026
mtGrasp
Public
mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
Python
•
GNU General Public License v3.0
•3•24•2•0•Updated Mar 26, 2026Mar 26, 2026
btl
Public
:microscope: Bioinformatics Technology Lab, Genome Sciences Centre
HTML
•3•2•4•0•Updated Mar 26, 2026Mar 26, 2026
ntJoin
Public
🔗Genome assembly scaffolder using minimizer graphs
Python
•
GNU General Public License v3.0
•13•85•1•0•Updated Mar 26, 2026Mar 26, 2026
ntStat
Public
ntStat: a toolkit for statistical analysis of k-mer frequency and depth
C++
•
GNU General Public License v3.0
•0•3•0•0•Updated Mar 25, 2026Mar 25, 2026
AIEdit
Public
Machine learning on spaced seed hit patterns for assembly polishing
C++
•
GNU General Public License v3.0
•0•0•0•0•Updated Mar 25, 2026Mar 25, 2026
ntSynt-viz
Public
Multi-genome synteny block visualization tool
Python
•
GNU General Public License v3.0
•4•55•1•0•Updated Mar 25, 2026Mar 25, 2026
straglr
Public
Tandem repeat expansion detection or genotyping from long-read alignments
bioinformatics genomics tandem-repeats
bioinformatics genomics tandem-repeats long-reads
Python
•
Other
•14•149•34•1•Updated Mar 25, 2026Mar 25, 2026
aakomp
Public
Fast, alignment-free genome completeness estimator
C++
•
GNU General Public License v3.0
•1•6•0•0•Updated Mar 24, 2026Mar 24, 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 24, 2026Mar 24, 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 24, 2026Mar 24, 2026
tigmint
Public
⛓ Correct misassemblies using linked AND long reads
bioinformatics genome-assembly genome-scaffolding
bioinformatics genome-assembly genome-scaffolding 10xgenomics misassembly-correction linked-reads bioinformatics-tool
Python
•
GNU General Public License v3.0
•13•63•1•0•Updated Mar 24, 2026Mar 24, 2026
pavfinder_transcriptome
Public
Python
•0•0•1•0•Updated Mar 24, 2026Mar 24, 2026
pavfinder
Public
:mag: Post Assembly Variants Finder
bioinformatics rna-seq assembly
bioinformatics rna-seq assembly structural-variants gene-fusions splice-variants
Python
•
Other
•5•18•1•0•Updated Mar 24, 2026Mar 24, 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
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++
•
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•105•0•0•Updated Mar 18, 2026Mar 18, 2026
AMPd-Up
Public
De novo antimicrobial peptide sequence generation with recurrent neural networks
Python
•
Other
•0•4•1•0•Updated Mar 17, 2026Mar 17, 2026
AMPlify
Public
Attentive deep learning model for antimicrobial peptide prediction
Python
•
Other
•13•56•4•0•Updated Mar 17, 2026Mar 17, 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
•
Other
•9•108•9•1•Updated Mar 13, 2026Mar 13, 2026
rAMPage
Public
rAMPage: Rapid AMP Annotation and Gene Estimation
Shell
•
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++
•
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++
•
MIT License
•9•78•9•2•Updated Mar 13, 2026Mar 13, 2026
ntEmbd
Public
Deep learning embedding for nucleotide sequences
Python
•
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
•
Other
•64•295•35•2•Updated Mar 12, 2026Mar 12, 2026

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Birol Lab

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All

92 repositories

ntRoot

abyss

LINKS

arcs

HLAminer

mtGrasp

btl

ntJoin

ntStat

AIEdit

ntSynt-viz

straglr

aakomp

physlr

RAILS

tigmint

pavfinder_transcriptome

pavfinder

Stash

goldrush

btllib

ntSynt

AMPd-Up

AMPlify

RNA-Bloom

rAMPage

ntHash

ntCard

ntEmbd

NanoSim

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Repositories list

92 repositories