Software

ABySS

brew install abyss
conda install -c bioconda abyss
docker run bcgsc/abyss

Scalable de novo genome assembler with short reads

ABySS-explorer

brew install brewsci/bio/abyss-explorer

Visual exploration of genome sequence assemblies

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

Memory efficient sequence read mapping with Bloom filters

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

Kollector

brew install brewsci/science/kollector

Targeted de novo gene assembly pipeline

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

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

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

PAVFinder

Python package to identify structural variants from de novo assemblies

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

Straglr

Short-tandem repeat genotyping using long 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

xmatchview

brew install brewsci/bio/xmatchview
conda install -c bioconda xmatchview
docker run quay.io/bcgsc_btl/xmatchview

Genome sequence alignment/synteny visualization