Genome assembly tools

List of genome assembly tools based on the one presented in the review: "A deep dive into genome assemblies of non-vertebrate animals." Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F. Peer Community Journal, 2022. doi:10.24072/pcjournal.128

Contributing

Adding a software can be done by adding a line in the corresponding CSV file:

• data/assemblers.csv for genome assemblers.
• data/processors.csv for assembly pre- or post-processing tools.

Modifications to this readme should be done in the template file of the corresponding section (see templates). Every month, a Github action automatically updates the README using the data and templates, fetching the latest commit date for each software.

Table of contents

• Genome assemblers
  • Sanger reads
  • High-accuracy short reads
  • Low-accuracy long reads
  • High-accuracy long reads
• Assembly pre and post-processing
  • Long-read error correction
  • Polishing
  • Haplotig purging
  • Scaffolding
  • Gap filling

Genome assemblers

Sanger reads

Assembler	Publication	Last update
ARACHNE	10.1101/gr.208902
Atlas	10.1101/gr.2264004	2013
CAP3	10.1101/gr.9.9.868
Celera	10.1093/bioinformatics/btn074
Euler	10.1073/pnas.171285098
JAZZ	10.1126/science.1072104
Minimus	10.1186/1471-2105-8-64
phrap	10.1101/gr.8.3.186
Phusion	10.1101/gr.731003
TIGR	10.1089/gst.1995.1.9

High-accuracy short reads

Assembler	Publication	Last update
ABySS	10.1101/gr.214346.116	2024-3
ALLPATHS	10.1101/gr.7337908	2008
BASE	10.1186/s12864-016-2829-5	2016-1
CABOG	10.1093/bioinformatics/btn548	2008
Edena	10.1101/gr.072033.107	2013
EPGA	10.1093/bioinformatics/btu762	2017-4
Euler-SR	10.1101/gr.7088808	2011
Gossamer	10.1093/bioinformatics/bts297	2012
IDBA	10.1007/978-3-642-12683-3_28	2016-12
ISEA	10.1109/TCBB.2016.2550433
JR-Assembler	10.1073/pnas.1314090110
LightAssembler	10.1093/bioinformatics/btw470
Meraculous	10.1371/journal.pone.0023501
Minia	10.1186/1748-7188-8-22	2023-11
Mira	10.1.1.23.7465
Newbler
PCAP	10.1101/gr.1390403
PE-Assembler	10.1093/bioinformatics/btq626
PERGA	10.1371/journal.pone.0114253
Platanus	10.1101/gr.170720.113
QSRA	10.1186/1471-2105-10-69
Ray	10.1089/cmb.2009.0238
Readjoiner	10.1186/1471-2105-13-82
SGA	10.1101/gr.126953.111
SHARCGS	10.1101/gr.6435207
SOAPdenovo	10.1101/gr.097261.109
SOAPdenovo2	10.1186/2047-217X-1-18
SPAdes	10.1089/cmb.2012.0021
SparseAssembler	10.1186/1471-2105-13-S6-S1
SSAKE	10.1093/bioinformatics/btl629
SUTTA	10.1093/bioinformatics/btq646
VCAKE	10.1093/bioinformatics/btm451
Velvet	10.1002/0471250953.bi1105s31
Taipan	10.1093/bioinformatics/btp374

Low-accuracy long reads

Assembler	Publication	Last update
Canu	10.1101/gr.215087.116	2024-4
FALCON	10.1038/nmeth.4035	2018-4
Flye	10.1038/s41587-019-0072-8	2024-3
GoldRush	10.1101/2022.10.25.513734	2024-4
HINGE	10.1101/gr.216465.116	2019-1
MECAT	10.1038/nmeth.4432	2019-2
MECAT2	10.1038/nmeth.4432	2020-4
miniasm	10.1038/nmeth.4432	2019-10
NECAT	10.1038/s41467-020-20236-7	2021-3
NextDenovo		2024-4
Ra	10.1109/ISPA.2019.8868909	2018-12
Raven	10.1038/s43588-021-00073-4	2023-11
SMARTdenovo	10.20944/preprints202009.0207.v1	2021-2
wtdbg		2017-3
wtdbg2	10.1038/s41592-019-0669-3	2020-12
shasta	10.1038/s41587-020-0503-6	2024-4

High-accuracy long reads

Assembler	Publication	Last update
Alice-asm		2024-4
Flye	10.1038/s41587-019-0072-8	2024-3
HiCanu	10.1101/gr.215087.116	2024-4
hifiasm	10.1038/s41592-020-01056-5	2024-4
IPA		2022-3
LJA	10.1101/2020.12.10.420448	2023-8
mdBG	10.1016/j.cels.2021.08.009	2023-1
MBG	10.1093/bioinformatics/btab004	2024-3
NextDenovo		2024-4
PECAT	10.1101/2022.09.25.509436	2024-4
Peregrine		2022-2
Raven	10.1038/s43588-021-00073-4	2023-11
verkko	10.1101/2022.06.24.497523	2024-4
wtdbg2	10.1038/s41592-019-0669-3	2020-12

Assembly pre and post-processing

Long-read error correction

Reads	Tool	Publication	Last update
Long reads	Canu	10.1101/gr.215087.116	2024-4
	CONSENT	10.1038/s41598-020-80757-5	2024-2
	Daccord	10.1101/106252	2018-9
	FLAS	10.1093/bioinformatics/btz206	2019-2
	HALC	10.1186/s12859-017-1610-3	2018-5
	MECAT	10.1038/nmeth.4432	2019-2
	MECAT2	10.1038/nmeth.4432	2020-4
	NECAT	10.1038/s41467-020-20236-7	2021-3
	NextDenovo		2024-4
Short reads	CoLoRMap	10.1093/bioinformatics/btw463	2018-3
	Hercules	10.1093/nar/gky724	2018-8
	HG-CoLoR	10.1093/bioinformatics/bty521	2021-1
	Jabba	10.1186/s13015-016-0075-7	2018-6
	LoRDEC	10.1093/bioinformatics/btu538	2020
	LoRMA	10.1093/bioinformatics/btw321	2019
	NaS	10.1186/s12864-015-1519-z	2017-3
	proovread	10.1093/bioinformatics/btu392	2019-5
	Ratatosk	10.1186/s13059-020-02244-4	2023-8

Polishing

Reads	Tool	Publication	Last update
Long reads	Arrow		2014
	CONSENT	10.1038/s41598-020-80757-5	2024-2
	GoldRush	10.1101/2022.10.25.513734	2024-4
	Quiver		2014
Long reads + short reads	Hapo-G	10.1093/nargab/lqab034	2024-3
	HyPo	10.1101/2019.12.19.882506	2020-2
	Racon	10.1101/gr.214270.116	2020-8
Short reads	ntEdit	10.1093/bioinformatics/btz400	2024-4
	Pilon	10.1371/journal.pone.0112963	2021-1
	POLCA	10.1371/journal.pcbi.1007981	2024-2
	Apollo	10.1093/bioinformatics/btaa179	2020-5

Haplotig purging

Reads	Tool	Publication	Last update
Long reads	HaploMerger2	10.1093/bioinformatics/btx220	2016-12
	purge_dups	10.1093/bioinformatics/btaa025	2023-12
	Purge Haplotigs	10.1186/s12859-018-2485-7	2024-2
Long reads + short reads	Redundans	10.1093/nar/gkw294	2023-12

Scaffolding

Reads	Tool	Publication	Last update
Genetic maps	ALLMAPS	10.1186/s13059-014-0573-1	2022
Hi-C	3D-DNA	10.1126/science.aal3327	2023-11
	dnaTri	10.1038/nbt.2768	2015-7
	EndHiC	10.48550/arXiv.2111.15411	2022-10
	GRAAL	10.1038/ncomms6695	2020-1
	HiCAssembler	10.1101/gad.328971.119	2019-11
	msscaf		2022-10
	instaGRAAL	10.1186/s13059-020-02041-z	2024-3
	Lachesis	10.1038/nbt.2727	2017-12
	pin_hic	10.1186/s12859-021-04453-5	2021-12
	SALSA2	10.1371/journal.pcbi.1007273	2022-4
	scaffHiC		2022-12
	YaHS		2023-6
Linked reads	ARBitR	10.1093/bioinformatics/btaa975	2020-10
	Architect	10.1093/bioinformatics/btw267	2016-10
	ARCS	10.1093/bioinformatics/btx675	2024-3
	ARKS	10.1186/s12859-018-2243-x	2019-12
	fragScaff	10.1101/gr.178319.114	2018-11
	scaff10X		2022-1
	SpLitteR		2022-12
	msscaf		2022-10
Long reads	DENTIST	10.1093/gigascience/giab100	2024-2
	FinisherSC	10.1093/bioinformatics/btv280	2016-11
	gapless	10.1101/2022.03.08.483466
	GoldRush	10.1101/2022.10.25.513734	2024-4
	LINKS	10.1186/s13742-015-0076-3	2023-12
	LRScaf	10.1186/s12864-019-6337-2	2021-11
	npScarf	10.1038/ncomms14515	2019-10
	PBJelly	10.1371/journal.pone.0047768	2017
	RAILS	10.21105/joss.00116	2023-12
	SLR	10.1186/s12859-019-3114-9	2020-8
	msscaf		2022-10
	SMIS		2018-2
	SMSC	10.1186/s12864-017-4271-8	2019-9
	SSPACE-LongRead	10.1186/1471-2105-15-211	2014
Mate pairs	BATISCAF	10.1101/330472
	BESST	10.1186/1471-2105-15-281
	BOSS	10.1093/bioinformatics/btw597
	GRASS	10.1093/bioinformatics/bts175
	MIP	10.1093/bioinformatics/btr562
	Opera	10.1089/cmb.2011.0170
	ScaffMatch	10.1093/bioinformatics/btv211
	ScaffoldScaffolder	10.1093/bioinformatics/btv548
	SCARPA	10.1093/bioinformatics/bts716
	SCOP	10.1093/bioinformatics/bty773
	SLIQ	10.1089/cmb.2011.0263
	SOPRA	10.1186/1471-2105-11-345
	SSPACE	10.1093/bioinformatics/btq683
	WiseScaffolder	10.1186/s12859-015-0705-y
Optical maps	AGORA	10.1186/1471-2105-13-189	2012
	BiSCoT	10.7717/peerj.10150	2020-11
	OMGS	10.1089/cmb.2019.0310	2018-11
	SewingMachine	10.1186/s12864-015-1911-8	2015
	SOMA	10.1093/bioinformatics/btn102	2008
Short reads	Bambus	10.1101/gr.1536204

Gap filling

Reads	Tool	Publication	Last update
Long reads	Cobbler	10.21105/joss.00116	2023-12
	DENTIST	10.1093/gigascience/giab100	2024-2
	FGAP	10.1186/1756-0500-7-371	2017-12
	FinisherSC	10.1093/bioinformatics/btv280	2016-11
	gapless	10.1101/2022.03.08.483466
	GMcloser	10.1093/bioinformatics/btv465	2018
	LR_Gapcloser	10.1093/gigascience/giy157	2018-9
	PBJelly	10.1371/journal.pone.0047768	2017
	PGcloser	10.1177/1176934320913859	2020
	TGS-GapCloser	10.1093/gigascience/giaa094	2023-12
	YAGCloser		2023-2
Short reads	GapFiller	10.1186/gb-2012-13-6-r56
	GAPPadder	10.1186/s12864-019-5703-4
	Sealer	10.1186/s12859-015-0663-4