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- Flye is a de novo assembler for single molecule sequencing reads
(https://github.com/fenderglass/Flye) - SMARTdenovo is an ultra-fast de novo assembler using long noisy reads
(https://github.com/ruanjue/smartdenovo) - bwa - Burrows-Wheeler Alignment Tool for mapping low-divergent sequences against a large reference genome
(http://bio-bwa.sourceforge.net/) - FREEC is a tool for the detection of copy-number changes and allelic imbalances using deep-sequencing data
(https://docs.hpc.qmul.ac.uk/apps/bio/freec/) - MergeMap constructs accurate consensus genetic maps from a set of individual genetic maps using DAGs
(http://www.oligospawn.org/mgmap/) - Canu is a hierarchical assembly pipeline for high-noise single-molecule sequencing
(https://github.com/marbl/canu) - Racon is a genomic consensus module to correct raw contigs generated by rapid assembly methods
(https://github.com/lbcb-sci/racon) - Unicycler is an assembly pipeline for bacterial genomes
(https://github.com/rrwick/Unicycler) - PanGenie - Genotyping based on k-mers and pangenome graphs
(https://bitbucket.org/jana_ebler/pangenie/src/master/) - Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA
(https://github.com/gmarcais/Jellyfish)