Quick links

Selected sequencing platforms

Pacific Biosciences (PacBio)

PacBio is a leading provider of advanced DNA sequencing technology.

♦ https://www.pacb.com/

Oxford Nanopore Technologies (ONT)

ONT stands front of DNA sequencing innovation through its groundbreaking nanopore sequencing technology.

♦ https://www.nanoporetech.net/

Illumina

Illumina is renowned for its innovative contributions to genetic research and diagnostics.

♦ https://www.illumina.com/

Beijing Genomics Institute or Huada Genomics Institute (BGI)

BGI specializes in large-scale DNA sequencing, bioinformatics analysis, and biotechnological applications.

♦ https://www.bgi.com/

Major assembly tools used in recent three years

Software for contig assembly stage

Canu: ♦ https://github.com/marbl/canu

Falcon: ♦ https://github.com/PacificBiosciences/FALCON

Hifiasm: ♦ https://github.com/chhylp123/hifiasm

NextDenovo: ♦ https://github.com/Nextomics/NextDenovo

wtdbg: ♦ https://github.com/ruanjue/wtdbg2

Software for polishing stage

Pilon: ♦ https://github.com/broadinstitute/pilon

Racon: ♦ https://github.com/isovic/racon

Arrow: ♦ https://github.com/PacificBiosciences/GenomicConsensus

Nextpolish: ♦ https://github.com/Nextomics/NextPolish

Quiver: ♦ https://github.com/PacificBiosciences/GenomicConsensus

Software for scaffolding stage

3D-DNA: ♦ https://github.com/aidenlab/3d-dna

LACHESIS: ♦ http://krishna.gs.washington.edu/LACHESIS/

ALLHIC: ♦ https://github.com/tangerzhang/ALLHiC

RagTag: ♦ https://github.com/malonge/RagTag

BioNano Solve: ♦ https://bionano.com/