De novo genome assembly

Hybrid error correction
Using short reads or short-read assemblies to correct raw long reads
Nanocorr (I and O) https://github.com/jgurtowski/nanocorr
MaSuRCA (I and P) https://github.com/alekseyzimin/masurca
PBcR (I and P) (also for just long reads) http://wgs-assembler.sourceforge.net/wiki/index.php?title=PBcR
Spades (I, P and O) https://github.com/ablab/spades

Self error correction
Correct raw long reads using other raw long reads
FALCON-sense (P) https://github.com/PacificBiosciences/FALCON
pbdagcon (P) https://github.com/PacificBiosciences/pbdagcon

Long-read overlapping
Find pairs of reads that align to each other
MHAP (P and O) https://github.com/marbl/MHAP
Minimap (P and O) https://github.com/lh3/minimap
DALIGNER (P and O) https://github.com/thegenemyers/DALIGNER

Contig assembly
Arrange reads that overlap with each other to build a consensus sequence
Canu (P and O) https://github.com/marbl/canu
FALCON (P) https://github.com/PacificBiosciences/FALCON
Hinge (P) https://github.com/HingeAssembler/HINGE
MECAT (P and O) https://github.com/xiaochuanle/MECAT
Miniasm (O and P) https://github.com/lh3/miniasm
Spades (I, P and O) https://github.com/ablab/spades
Supernova (G) https://support.10xgenomics.com/de-novo-assembly/software/overview/welcome
HGAP (P) https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP
Flye (P) https://github.com/fenderglass/Flye
MARVEL (P) https://github.com/schloi/MARVEL

Scaffolding
Order and orient contigs into chromosome sequences
Architect (I) https://github.com/kuleshov/architect
ARCS (G) https://github.com/bcgsc/arcs
BioNano Access (B) https://bionanogenomics.com/support-page/bionano-access/
FragScaff (H) https://sourceforge.net/projects/fragscaff/
LINKS (P and O) https://github.com/warrenlr/LINKS
npScarf (O) https://github.com/mdcao/npScarf
RAILS (P and O) https://github.com/bcgsc/RAILS
SALSA (H) https://github.com/machinegun/SALSA

Gap filling
Localized alignment and assembly to improve an existingassembly
PBJelly (P) https://sourceforge.net/p/pb-jelly
RAILS and Cobbler (P and O) https://github.com/bcgsc/RAILS

Polishing
Refine the consensus sequence of a de novo assembly by a reanalysis of how the raw reads align
Arrow (A and P) http://www.pacb.com/
Nanopolish (A and O) https://github.com/jts/nanopolish
Pilon (A and I) https://github.com/broadinstitute/pilon
Quiver (A and P) https://github.com/PacificBiosciences/GenomicConsensus
Racon (A, P and O) https://github.com/isovic/racon

注：A, assembly-based; B, BioNano Genomics; G, 10X Genomics; H, Hi-C; I, Illumina; O, Oxford Nanopore; P, PacBio;

补充：

1.Nanopore测序结果的分析大概流程：

2.三代样本数据集

https://github.com/PacificBiosciences/DevNet/wiki/Datasets