Software

ABySS

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

Scalable de novo genome assembler with short reads

ARCS

brew install brewsci/bio/arcs

Genome scaffolder by linked read alignment

ARKS

Genome scaffolder by linked read kmer mapping

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/alignment stages on a compute farm

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 error-rich DNA sequences

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

ntHash

Recursive hashing algorithm tuned for processing DNA/RNA sequences

PAVFinder

Python package to identify structural variants from de novo assemblies

Cobbler/RAILS

Gap-filling (cobbler) and scaffolding (RAILS) by long DNA sequence alignment

Tigmint

brew install brewsci/bio/tigmint
conda install -c bioconda tigmint
docker run bcgsc/tigmint

Misassembly correction utility with linked reads

Trans-ABySS

brew install brewsci/science/trans-abyss
conda install transabyss
docker run quay.io/biocontainers/transabyss

De novo transcriptome assembler

xmatchview

Genome sequence alignment visualization