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