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.

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
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
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	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	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	GapPredict LSTM character-level language model for genome assembly gap filling
GoldRush conda install -c bioconda goldrush docker run quay.io/biocontainers/goldrush Linear time complexity de novo long read genome assembler	HLAminer HLA predictions from DNA/RNA sequencing data
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	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	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	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	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	ntRoot conda install -c bioconda ntroot docker run quay.io/biocontainers/ntroot Ancestry predictions from genomic data
ntStat conda install bioconda::ntstat docker run quay.io/biocontainers/ntstat A toolkit for statistical analysis of k-mer frequency and depth	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	PASS conda install -c bioconda pass docker run quay.io/biocontainers/pass Protein Assembler with Short [peptide] Sequences
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
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
rAMPage Rapid AMP Annotation and Gene Estimation	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	SARS-CoV-2 Variants Timemaps Interactive SVG maps of DNA variations in SARS genomes over time and space
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
Straglr conda install -c bioconda straglr docker run quay.io/biocontainers/straglr Short-tandem repeat genotyping using long reads	tAMPer AMP toxicity prediction with a structure-aware deep learning model
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
Trans-ABySS brew install brewsci/science/trans-abyss conda install transabyss docker run quay.io/biocontainers/transabyss De novo transcriptome assembler with short reads	unikseq conda install -c bioconda unikseq docker run quay.io/biocontainers/unikseq Unique region identification in DNA sequences, using k-mers
xmatchview brew install brewsci/bio/xmatchview conda install -c bioconda xmatchview docker run quay.io/biocontainers/xmatchview Genome sequence alignment/synteny visualization