全基因组组装,注释与评估软件
全基因组组装,注释与评估软件集锦(更新于2020.03.20)
1.Assembly
1.1质体基因组
1.1.1NOVOPlasty
program language:Perl
Reference:
10.1093/nar/gkw955(Nucleic Acids Research ,2016)
10.1093/nargab/lqz011(NAR Genomics and Bioinformatics,2020)
Manual:https://github.com/ndierckx/NOVOPlasty
Link:https://github.com/ndierckx/NOVOPlasty
1.1.2GetOrganelle
program language:Python
Reference:10.1101/256479(bioRxiv ,2019)
Manual:https://github.com/Kinggerm/GetOrganelle
Link:https://github.com/Kinggerm/GetOrganelle
1.2核基因组
1.2.1Velvet
program language:C
Algorithm:De Bruijn graph(DBG)
Reference:
10.1101/gr.074492.107(Genome Research ,2008)
10.1371/journal.pone.0008407(Plos One,2009)
Manual:
https://www.ebi.ac.uk/~zerbino/velvet/velvet_poster.pdfhttps://www.ebi.ac.uk/~zerbino/velvet/Manual.pdfhttps://github.com/dzerbino/velvet/blob/master/Manual.pdf
Link:
https://github.com/dzerbino/velvethttps://www.ebi.ac.uk/~zerbino/velvet/
1.2.2HGAP
Reference:10.1038/nmeth.2474(Nature Methods ,2013)
Manual:
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-1.4https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP
Link:https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-1.4
1.2.3Falcon
program language:Python
Reference:10.1038/nmeth.4035(Nature Methods,2016)
Manual:https://github.com/PacificBiosciences/FALCON/wiki/Manual
Link:https://github.com/PacificBiosciences/FALCON
1.2.4Miniasm
program language:C
Reference:10.1093/bioinformatics/btw152(Bioinformatics,2016)
Manual:https://github.com/lh3/miniasm/blob/master/README.md
Link:https://github.com/lh3/miniasm/
1.2.5CANU
program language:C++
Reference:10.1101/gr.215087.116(Genome Research,2017)
Manual:https://github.com/marbl/canu/blob/master/documentation/source/tutorial.rst
Link:https://github.com/marbl/canu
1.2.6Hinge
program language:C++
Reference:10.1101/gr.216465.116(Genome Research,2017)
Manual:https://github.com/HingeAssembler/HINGE
Link:https://github.com/HingeAssembler/HINGE
1.2.7racon
program language:C++
Reference:10.1101/gr.214270.116(Genome Research,2017)
Manual:https://github.com/isovic/racon
Link:https://github.com/isovic/racon
1.2.8MECAT
program language:C++
Reference: 10.1038/nmeth.4432(Nature Maethods,2017)
Manual:https://github.com/xiaochuanle/MECAT
Link:https://github.com/xiaochuanle/MECAT
1.2.9SMARTdenovo
program language:C
Reference:no publication informations
Manual:https://yiweiniu.github.io/blog/2018/04/Genome-Assembly-Pipeline-SMARTdenovo/
Link:https://github.com/ruanjue/smartdenovo
1.2.10SOAPdenovo2
program language:C
Reference:no publication informations
Manual:https://github.com/aquaskyline/SOAPdenovo2
Link:https://github.com/aquaskyline/SOAPdenovo2
1.2.11wtdbg2-MPI
program language:C
Reference:
10.1101/530972(bioRxiv,2019)
10.1038/s41592-019-0669-3(Nature Methods,2019)
Manual:https://github.com/ruanjue/wtdbg2/blob/master/README-ori.md
Link:https://github.com/qzwlecr/wtdbg2-MPI
2.Annotation
2.1质体基因组
2.1.1GeSeq
Reference: 10.1093/nar/gkx391(Nucleic Acids Research,2017)
Manual:
https://chlorobox.mpimp-golm.mpg.de/gs_documentation.htmlhttp://blog.sciencenet.cn/blog-3406804-1192085.html
Link:https://chlorobox.mpimp-golm.mpg.de/geseq.html
2.1.2PGA(Plastid Genome Annotator)
program language:Perl
Reference: 10.1186/s13007-019-0435-7(Plant Methods,2019)
Manual:
https://github.com/quxiaojian/PGAhttps://www.jianshu.com/p/6ac8a9fad9c9http://blog.sciencenet.cn/blog-3406804-1198528.html
Link:https://github.com/quxiaojian/PGA
2.2核基因组
2.2.1RepeatMasker(for repeat sequence)
program language:Perl
Reference:Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0.2013-2015 http://www.repeatmasker.org.
Manual:http://www.repeatmasker.org/webrepeatmaskerhelp.html
Link:http://www.repeatmasker.org/RMDownload.html
2.2.2BRAKER(for gene structure)
program language:Perl
Reference:
10.1186/1471-2105-7-62(BMC Bioinformatics,2006)
10.1093/bioinformatics/btn013(Bioinformatics,2008)
10.1093/bioinformatics/btv661(Bioinformatics,2016)
10.1007/978-1-4939-9173-0_5,1962:65-95(Methods in Molecular Biology,2019)
Manual:https://github.com/Gaius-Augustus/BRAKER
Link:https://github.com/Gaius-Augustus/BRAKER
2.2.3Maker (for gene structure)
Reference:10.1101/gr.6743907(Genome Research,2008)
Manual:
https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Pagehttp://gmod.org/wiki/MAKER_Tutorial
Link:http://www.yandell-lab.org/software/maker.html
2.2.4MAKER-P (for gene structure)
Reference:no pubilished info
Manual:https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page
Link:http://www.yandell-lab.org/software/maker-p.html
2.2.5eggNOG-mapper(for gene function)
program language:Python
Reference:
10.1093/molbev/msx148(Molecular Biology and Evolution,2017)10.1093/nar/gky1085(Nucleic Acids Research,2019)
Manual:https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2
Link:
http://eggnog-mapper.embl.de/
https://github.com/eggnogdb/eggnog-mapper
3.Correction
3.1pilon
program language:Scala
Reference:10.1371/journal.pone.0112963(PLoS ONE,2014)
Manual:https://github.com/broadinstitute/pilon/wiki/Methods-of-Operation
Link:https://github.com/broadinstitute/pilon
3.2redundans
program language:Perl
Reference:10.1093/nar/gkw294(Nucleic Acids Research,2016)
Manual:
https://github.com/lpryszcz/redundans/blob/master/docs/poster.pdfhttps://github.com/lpryszcz/redundans
Link:https://github.com/lpryszcz/redundans
3.3TGS-GapCloser
program language:C++
Reference:10.1101/831248(bioRxiv,2019)
Manual:https://github.com/BGI-Qingdao/TGS-GapCloser
Link:https://github.com/BGI-Qingdao/TGS-GapCloser
4.Evaluation
BUSCO
Reference:10.1007/978-1-4939-9173-0_14(Methods in Molecular Biology,2019)
Manual:https://busco.ezlab.org/busco_userguide.html
Link:https://github.com/c-omics/busco
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