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Genome assembly tools

If you appreciate this work, please cite: "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:

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

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 2024-10
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 2024-10
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 2024-11
FALCON 10.1038/nmeth.4035 2018-4
Flye 10.1038/s41587-019-0072-8 2024-8
GoldRush 10.1101/2022.10.25.513734 2024-11
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 10.1186/s13059-024-03252-4 2024-5
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 2024-11

High-accuracy long reads

Assembler Publication Last update
Alice-asm 2024-8
Flye 10.1038/s41587-019-0072-8 2024-8
HiCanu 10.1101/gr.215087.116 2024-11
hifiasm 10.1038/s41592-020-01056-5 2024-11
IPA 2022-3
LJA 10.1101/2020.12.10.420448 2023-8
mdBG 10.1016/j.cels.2021.08.009 2024-9
MBG 10.1093/bioinformatics/btab004 2024-3
NextDenovo 10.1186/s13059-024-03252-4 2024-5
PECAT 10.1101/2022.09.25.509436 2024-5
Peregrine 2022-2
Raven 10.1038/s43588-021-00073-4 2023-11
verkko 10.1101/2022.06.24.497523 2024-11
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 2024-11
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 2024-5
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 2024-9

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 2024-11
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 2024-11
Pilon 10.1371/journal.pone.0112963 2021-1
POLCA 10.1371/journal.pcbi.1007981 2024-10
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
AutoHiC 10.1101/2023.08.27.555031 2024-9
dnaTri 10.1038/nbt.2768 2015-7
EndHiC 10.48550/arXiv.2111.15411 2022-10
GRAAL 10.1038/ncomms6695 2020-1
GreenHill 10.1186/s13059-023-03006-8 2024-3
HapHiC 10.1101/2023.11.18.567668 2024-10
HiCAssembler 10.1101/gad.328971.119 2024-9
instaGRAAL 10.1186/s13059-020-02041-z 2024-3
Lachesis 10.1038/nbt.2727 2017-12
msscaf 2022-10
pin_hic 10.1186/s12859-021-04453-5 2021-12
SALSA2 10.1371/journal.pcbi.1007273 2024-5
scaffHiC 2022-12
YaHS 2024-11
Linked reads ARBitR 10.1093/bioinformatics/btaa975 2020-10
Architect 10.1093/bioinformatics/btw267 2016-10
ARCS 10.1093/bioinformatics/btx675 2024-11
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 2024-11
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 2024-9
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