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.

Antimicrobial Peptide (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 Deep learning model for AMP prediction	AMPSeek       AMP prediction, 3D structure, toxicity detection
rAMPage       Rapid AMP Annotation and Gene Estimation	tAMPer       Peptide toxicity prediction	triAMPh       Heterogeneous graph networks in AMP predictions
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 w/minimizers	unikseq   conda install -c bioconda unikseq docker run quay.io/biocontainers/unikseq Unique region identification in DNA sequences
Genome Analysis
aaKomp   conda install -c bioconda aakomp docker run quay.io/biocontainers/aakomp Genome completeness estimator	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
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
Genome Assembly
ABySS brew install abyss conda install -c bioconda abyss docker run quay.io/biocontainers/abyss Scalable short reads de novo genome assembler	AIEdit       Machine learning-based 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
GoldPolish       Genome sequence polisher w/long reads	GoldRush   conda install -c bioconda goldrush docker run quay.io/biocontainers/goldrush Linear time complexity long read genome assembly	Konnector brew install abyss conda install -c bioconda abyss docker run bcgsc/abyss Connecting paired-end reads w/Bloom filter graphs
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 Assembly correction+scaffolding w/long reads	mtGrasp   conda install -c bioconda mtgrasp docker run quay.io/biocontainers/mtgrasp Mitochondrial genome assembly + standardization
Polisher brew install brewsci/bio/nthits ntedit abyss conda install -c bioconda nthits ntedit abyss   Targeted polishing+automated 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 w/minimizer graphs
ntLink brew install brewsci/bio/ntlink conda install -c bioconda ntlink docker run quay.io/biocontainers/ntlink Long read genome scaffolding w/minimizers	Physlr   conda install -c bioconda physlr docker run quay.io/biocontainers/physlr Scaffolding w/linked read physical map	Cobbler/RAILS brew install brewsci/bio/rails     Gap-filling + scaffolding w/long reads
Sealer brew install abyss conda install -c bioconda abyss docker run quay.io/biocontainers/abyss Gap-closing for finishing draft genomes	Tigmint brew install brewsci/bio/tigmint conda install -c bioconda tigmint docker run quay.io/biocontainers/tigmint Misassembly correction w/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 Assembler for bulk, single-cell & nanopore RNA-seq	RNA-Scoop       Single-cell transcriptomes isoform visualization
Utilities
aaHash   conda install -c bioconda btllib docker run quay.io/biocontainers/btllib Hashing algorithm for amino acid sequences	BioBloomTools brew install brewsci/bio/biobloomtools conda install -c bioconda biobloomtools docker run quay.io/biocontainers/biobloomtools Sequence read mapping w/Bloom filters	btllib   conda install -c bioconda btllib docker run quay.io/biocontainers/btllib Sequence processing C++ library, with Python API
MAP       Microdilution Assay Processor	NanoSim   conda install -c bioconda nanosim docker run quay.io/biocontainers/nanosim Nanopore sequence simulator	ntCard brew install brewsci/bio/ntcard conda install -c bioconda ntcard docker run quay.io/biocontainers/ntcard k-mer cardinality estimation in genomics datasets
ntHash       Hashing algorithm for DNA/RNA	ntStat   conda install bioconda::ntstat docker run quay.io/biocontainers/ntstat Statistical analysis of k-mers	SARS-CoV-2 Variants Timemaps       SARS genome variant maps over time & space
Vintage
ABySS-explorer brew install brewsci/bio/abyss-explorer     Visual exploration of genome sequence assemblies	ChopStitch       De novo exon prediction and splice graph	DIDA brew install brewsci/bio/dida     Distribution of sequence indexing/alignments
GapPredict       LSTM model for genome gap filling	Kollector brew install brewsci/science/kollector     Targeted de novo gene assembly pipeline	ntHits brew install brewsci/bio/nthits conda install -c bioconda nthits docker run quay.io/biocontainers/nthits Repeat k-mer identification in DNA sequencing data
PAVFinder   conda install -c bioconda pavfinder docker run quay.io/biocontainers/pavfinder Structural variants identification	SSAKE   conda install -c bioconda ssake docker run quay.io/biocontainers/ssake Short read genome assembler	TASR       Targeted Assembly of Sequence Reads
Trans-ABySS brew install brewsci/science/trans-abyss conda install transabyss docker run quay.io/biocontainers/transabyss De novo transcriptome assembler with short reads	xmatchview brew install brewsci/bio/xmatchview conda install -c bioconda xmatchview docker run quay.io/biocontainers/xmatchview Genome sequence alignment/synteny visualization