Genome assemblers

Genome assemblers

List of genome assembly programs for PacBio long-read datasets. Not in any specific order :D
Some of the assemblers are suitable also for ONT reads.

1. Hifiasm

https://github.com/chhylp123/hifiasm
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads.

1. IPA

https://github.com/PacificBiosciences/pbipa
https://github.com/PacificBiosciences/pbbioconda/wiki/Improved-Phased-Assembler
Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly.

1. CANU

https://github.com/marbl/canu
Canu Tutorial — canu 2.2 documentation
Canu assembles reads from PacBio RS II or Oxford Nanopore MinION instruments into uniquely-assemblable contigs, unitigs. Both raw and Hifi reads supported.

1. FALCON

https://github.com/PacificBiosciences/pb-assembly
FALCON and FALCON-Unzip are de novo genome assemblers for PacBio long reads, also known as Single-Molecule Real-Time (SMRT) sequences. Both raw and Hifi reads supported.

1. Wtdbg2

https://github.com/ruanjue/wtdbg2
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). Both raw and Hifi reads supported.

1. Flye

https://github.com/fenderglass/Flye
Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. Both raw and Hifi reads supported.