Software ABySS brew install abyss conda install -c bioconda abyss docker run bcgsc/abyssScalable de novo genome assembler with short reads ABySS-explorer brew install brewsci/bio/abyss-explorerVisual 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/amplifyAttentive deep learning model for antimicrobial peptide prediction ARCS / ARKS brew install brewsci/bio/arcs conda install -c bioconda arcs docker run quay.io/biocontainers/arcsGenome scaffolder with long or linked reads BioBloom Tools brew install brewsci/bio/biobloomtools conda install -c bioconda biobloomtools docker run quay.io/biocontainers/biobloomtoolsMemory efficient sequence read mapping with Bloom filters btllib conda install -c bioconda btllib docker run quay.io/biocontainers/btllibGenomic sequence processing common code C++ library, with Python API ChopStitch De novo exon prediction and splicegraph construction DIDA brew install brewsci/bio/didaSequence 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/goldrushLinear time complexity de novo long read genome assembler Kollector brew install brewsci/science/kollectorTargeted de novo gene assembly pipeline Konnector brew install abyss conda install -c bioconda abyss docker run bcgsc/abyssConnecting 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/linksAlignment-free genome scaffolder with long reads LongStitch conda install -c bioconda longstitch docker run quay.io/biocontainers/longstitchGenome assembly correction+scaffolding with long reads NanoSim conda install -c bioconda nanosim docker run quay.io/biocontainers/nanosimNanopore read sequence simulator, guided by technology-specific features ntCard brew install brewsci/bio/ntcard conda install -c bioconda ntcard docker run quay.io/biocontainers/ntcardStreaming algorithm for cardinality estimation in genomics datasets Genome sequence polishing protocol brew install brewsci/bio/nthits ntedit abyss conda install -c bioconda nthits ntedit abyssTargeted error resolution, automated genome finishing ntEdit brew install brewsci/bio/ntedit conda install -c bioconda ntedit docker run quay.io/biocontainers/nteditFast 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/nthitsRepeat kmer identification in high-throughput DNA sequencing data ntJoin brew install brewsci/bio/ntjoin conda install -c bioconda ntjoin docker run quay.io/biocontainers/ntjoinAssembly-guided scaffolding using minimizer graphs ntLink brew install brewsci/bio/ntlink conda install -c bioconda ntlink docker run quay.io/biocontainers/ntlinkGenome 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/pavfinderPython package to identify structural variants from de novo assemblies peekseq De novo protein-coding potential predictor Physlr conda install -c bioconda physlr docker run quay.io/biocontainers/physlrChromosome-scale de novo scaffolding using physical map of linked reads Cobbler/RAILS brew install brewsci/bio/railsGap-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/rnabloomLightweight 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/abyssscalable gap-closing application for finishing draft genomes SSAKE conda install -c bioconda ssake docker run quay.io/biocontainers/ssakeDe novo Genome Assembler with Short Sequence Reads Straglr conda install -c bioconda straglr docker run quay.io/biocontainers/straglrShort-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/tigmintMisassembly correction utility with long or linked reads Trans-ABySS brew install brewsci/science/trans-abyss conda install transabyss docker run quay.io/biocontainers/transabyssDe novo transcriptome assembler with short reads unikseq conda install -c bioconda unikseqUnique 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/xmatchviewGenome sequence alignment/synteny visualization