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

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 splicegraph 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

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

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

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/bcgsc_btl/xmatchview

Genome sequence alignment/synteny visualization