Make Longer Contigs - Githubissues

averagehat / pathos

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Make Longer Contigs #6

Open averagehat opened 5 years ago

averagehat commented 5 years ago

@mousepixels

GapFiller could be an option

Warning: https://www.biostars.org/p/86705/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826002/

To check the accuracy of genome assembly, the contigs were aligned to their related reference genomes using QUAST tool

GAPPadder, GapCloser, GapFiller and Sealer https://sites.google.com/site/ishengtsai/image https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-4-r41

There are a few in silico tools that can fill in the gaps within scaffolds;

GapFiller (developed by myself, I'm also the developer of SSPACE): http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/ http://genomebiology.com/2012/13/6/R56

IMAGE2: http://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page

GapCloser (part of SOAP): http://sourceforge.net/projects/soapdenovo2/files/GapCloser/

https://www.biorxiv.org/content/biorxiv/early/2018/08/16/393116.full.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559175/

https://github.com/vibansal/hapcut may do something relevant