Resources

Here you will find cutting-edge technologies and resources developed by the Birol Lab to empower researchers in genomics, bioinformatics, life sciences and medical research and designed to streamline big data analysis, enhance data interpretation, and accelerate scientific discovery.

AMP Discovery
AMPd-up   conda install -c bioconda ampd-up docker run quay.io/biocontainers/ampd-up De novo AMP sequence generation with RNNs	AMPlify   conda install -c bioconda amplify docker run quay.io/biocontainers/amplify Attentive deep learning model for antimicrobial peptide prediction	AMPSeek       Anti-microbial property, protein structure and toxicity detection from peptide sequences
rAMPage       Rapid AMP Annotation and Gene Estimation	tAMPer       AMP toxicity prediction with a structure-aware deep learning model	triAMPh       TaRget Identification of AntiMicrobial Peptides with Heterogeneous graph attention networks
Comparative Genomics
ntSynt-viz   conda install -c bioconda ntsynt-viz   Multi-genome synteny visualization framework	ntSynt   conda install -c bioconda ntsynt docker run quay.io/biocontainers/ntsynt Multi-genome synteny detection using minimizer graph mapping	xmatchview brew install brewsci/bio/xmatchview conda install -c bioconda xmatchview docker run quay.io/biocontainers/xmatchview Genome sequence alignment/synteny visualization
Genome Analysis
aaKomp   conda install -c bioconda aakomp docker run quay.io/biocontainers/aakomp Fast, alignment-free genome completeness estimator	ChopStitch       De novo exon prediction and splice graph construction	DIDA brew install brewsci/bio/dida     Sequence alignment pipeline to distribute indexing/alignments on compute farms
HLAminer       HLA predictions from DNA/RNA sequencing data	ntRoot   conda install -c bioconda ntroot docker run quay.io/biocontainers/ntroot Ancestry predictions from genomic data	PAVFinder   conda install -c bioconda pavfinder docker run quay.io/biocontainers/pavfinder Python package to identify structural variants from de novo assemblies
peekseq   conda install -c bioconda peekseq docker run quay.io/biocontainers/peekseq De novo protein-coding potential predictor	Straglr   conda install -c bioconda straglr docker run quay.io/biocontainers/straglr Short-tandem repeat genotyping using long reads	unikseq   conda install -c bioconda unikseq docker run quay.io/biocontainers/unikseq Unique region identification in DNA sequences, using k-mers
Genome Assembly
ABySS brew install abyss conda install -c bioconda abyss docker run quay.io/biocontainers/abyss Scalable de novo genome assembler with short reads	ABySS-explorer brew install brewsci/bio/abyss-explorer     Visual exploration of genome sequence assemblies	AIEdit       Machine learning-based alignment-free genome polisher
ARCS / ARKS brew install brewsci/bio/arcs conda install -c bioconda arcs docker run quay.io/biocontainers/arcs Genome scaffolder with long or linked reads	GapPredict       LSTM character-level language model for genome assembly gap filling	GoldPolish       Genome sequence polisher with long sequencing reads
GoldRush   conda install -c bioconda goldrush docker run quay.io/biocontainers/goldrush Linear time complexity de novo long read genome assembler	Kollector brew install brewsci/science/kollector     Targeted de novo gene assembly pipeline	Konnector brew install abyss conda install -c bioconda abyss docker run bcgsc/abyss Connecting paired-end reads using a bloom filter de Bruijn graph
LINKS brew install brewsci/bio/links-scaffolder conda install -c bioconda links docker run quay.io/biocontainers/links Alignment-free genome scaffolder with long reads	LongStitch   conda install -c bioconda longstitch docker run quay.io/biocontainers/longstitch Genome assembly correction+scaffolding with long reads	mtGrasp   conda install -c bioconda mtgrasp docker run quay.io/biocontainers/mtgrasp Mitochondrial genome assembly and standardization pipeline
Genome sequence polishing protocol brew install brewsci/bio/nthits ntedit abyss conda install -c bioconda nthits ntedit abyss   Targeted error resolution, automated genome finishing	ntEdit brew install brewsci/bio/ntedit conda install -c bioconda ntedit docker run quay.io/biocontainers/ntedit Fast and scalable genome sequence polisher	ntJoin brew install brewsci/bio/ntjoin conda install -c bioconda ntjoin docker run quay.io/biocontainers/ntjoin Assembly-guided scaffolding using minimizer graphs
ntLink brew install brewsci/bio/ntlink conda install -c bioconda ntlink docker run quay.io/biocontainers/ntlink Genome assembly scaffolding using long reads and minimizers	Physlr   conda install -c bioconda physlr docker run quay.io/biocontainers/physlr Chromosome-scale de novo scaffolding using physical map of linked reads	Cobbler/RAILS brew install brewsci/bio/rails     Gap-filling (cobbler) and scaffolding (RAILS) with long reads
Sealer brew install abyss conda install -c bioconda abyss docker run quay.io/biocontainers/abyss scalable gap-closing application for finishing draft genomes	SSAKE   conda install -c bioconda ssake docker run quay.io/biocontainers/ssake De novo Genome Assembler with Short Sequence Reads	TASR       Targeted Assembly of Sequence Reads
Tigmint brew install brewsci/bio/tigmint conda install -c bioconda tigmint docker run quay.io/biocontainers/tigmint Misassembly correction utility with long or linked reads
Protein Analysis
PASS   conda install -c bioconda pass docker run quay.io/biocontainers/pass Protein Assembler with Short [peptide] Sequences
Transcriptome Assembly
RNA-Bloom   conda install -c bioconda rnabloom docker run quay.io/biocontainers/rnabloom Lightweight reference-free assembler for bulk, single-cell & nanopore RNA-seq data	RNA-Scoop       Interactive isoform visualization tool for single-cell transcriptomes	Trans-ABySS brew install brewsci/science/trans-abyss conda install transabyss docker run quay.io/biocontainers/transabyss De novo transcriptome assembler with short reads
Utilities
BioBloom Tools brew install brewsci/bio/biobloomtools conda install -c bioconda biobloomtools docker run quay.io/biocontainers/biobloomtools Memory efficient sequence read mapping with Bloom filters	btllib   conda install -c bioconda btllib docker run quay.io/biocontainers/btllib Genomic sequence processing common code C++ library, with Python API	MAP       Microdilution Assay Processor
NanoSim   conda install -c bioconda nanosim docker run quay.io/biocontainers/nanosim Nanopore read sequence simulator, guided by technology-specific features	ntCard brew install brewsci/bio/ntcard conda install -c bioconda ntcard docker run quay.io/biocontainers/ntcard Streaming algorithm for cardinality estimation in genomics datasets	ntHash       Recursive hashing algorithm tuned for processing DNA/RNA sequences
ntHits brew install brewsci/bio/nthits conda install -c bioconda nthits docker run quay.io/biocontainers/nthits Repeat kmer identification in high-throughput DNA sequencing data	ntStat   conda install bioconda::ntstat docker run quay.io/biocontainers/ntstat A toolkit for statistical analysis of k-mer frequency and depth	SARS-CoV-2 Variants Timemaps       Interactive SVG maps of DNA variations in SARS genomes over time and space