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 |
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