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•1•1•Updated Jun 11, 2026Jun 11, 2026
ntSynt-viz
Public
Multi-genome synteny block visualization tool
Python
•
GNU General Public License v3.0
•4•58•1•0•Updated Jun 11, 2026Jun 11, 2026
AMPSeek
Public
Antimicrobial property, protein structure and toxicity detection from peptide sequences
Python
•0•2•0•0•Updated Jun 10, 2026Jun 10, 2026
ntSynt
Public
Detecting multi-genome synteny using minimizer graph mapping
Python
•
GNU General Public License v3.0
•2•107•0•0•Updated Jun 5, 2026Jun 5, 2026
btl
Public
:microscope: Bioinformatics Technology Lab, Genome Sciences Centre
HTML
•3•2•4•0•Updated Jun 4, 2026Jun 4, 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 Jun 4, 2026Jun 4, 2026
PASS
Public
Proteome Assembler with Short peptide Sequence
Perl
•
GNU General Public License v3.0
•2•9•0•0•Updated Jun 4, 2026Jun 4, 2026
unikseq
Public
🧬 Unique (& conserved) DNA sequence identification
Perl
•
GNU General Public License v3.0
•1•19•0•0•Updated Jun 4, 2026Jun 4, 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•56•0•0•Updated Jun 4, 2026Jun 4, 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 Jun 4, 2026Jun 4, 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++
•
GNU General Public License v3.0
•10•73•0•0•Updated Jun 4, 2026Jun 4, 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
•
GNU General Public License v2.0
•11•26•0•0•Updated Jun 4, 2026Jun 4, 2026
AMPlify
Public
Attentive deep learning model for antimicrobial peptide prediction
Python
•
Other
•16•64•3•0•Updated Jun 2, 2026Jun 2, 2026
TASR
Public archive
Targeted Assembly of Short Reads
assembler short-reads targeted-assembly
assembler short-reads targeted-assembly
Perl
•
GNU General Public License v2.0
•0•7•0•0•Updated May 22, 2026May 22, 2026
AIEdit
Public
Machine learning on spaced seed hit patterns for assembly polishing
C++
•
GNU General Public License v3.0
•0•2•0•0•Updated Apr 30, 2026Apr 30, 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•29•25•8•Updated Apr 30, 2026Apr 30, 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 Apr 30, 2026Apr 30, 2026
triAMPh
Public
TaRget Identification of AntiMicrobial Peptides with Heterogeneous graph attention networks
Python
•
MIT License
•0•1•0•0•Updated Apr 15, 2026Apr 15, 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•108•2•3•Updated Apr 2, 2026Apr 2, 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 Apr 1, 2026Apr 1, 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•2•0•Updated Apr 1, 2026Apr 1, 2026
ntLink
Public
Minimizer-based assembly scaffolding and mapping using long reads
bioinformatics assembly scaffolding
bioinformatics assembly scaffolding long-reads minimizers
Python
•
GNU General Public License v3.0
•8•51•0•0•Updated Apr 1, 2026Apr 1, 2026
ntJoin
Public
🔗Genome assembly scaffolder using minimizer graphs
Python
•
GNU General Public License v3.0
•13•88•0•0•Updated Apr 1, 2026Apr 1, 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 Apr 1, 2026Apr 1, 2026
LongStitch
Public
🪡Correct and scaffold assemblies using long reads
Makefile
•
GNU General Public License v3.0
•8•58•2•0•Updated Apr 1, 2026Apr 1, 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
ntStat
Public
ntStat: a toolkit for statistical analysis of k-mer frequency and depth
C++
•
GNU General Public License v3.0
•0•8•0•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•159•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
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•64•1•0•Updated Mar 24, 2026Mar 24, 2026

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Birol Lab

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All

92 repositories

ntRoot

ntSynt-viz

AMPSeek

ntSynt

btl

peekseq

PASS

unikseq

HLAminer

LINKS

ntEdit

SSAKE

AMPlify

TASR

AIEdit

btllib

abyss

triAMPh

ntHash

RAILS

physlr

ntLink

ntJoin

arcs

LongStitch

mtGrasp

ntStat

straglr

aakomp

tigmint

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Repositories list

92 repositories