Question

Assembly of wheat genome

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6.3 years ago

mustafa_aljadi ▴ 10

Hey All, I am working on the DNA assembly of the wheat genome. I used the W2rap assembler, the assembly is done. But I dont know how to determine if my assembly is good or Not? I mean which criteria I should follow? Thanks in advance Mustafa

genome • 1.9k views

ADD COMMENT • link updated 6.3 years ago by shengweima ▴ 60 • written 6.3 years ago by mustafa_aljadi ▴ 10

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Thank you so much guys for your help. Mustafa

ADD REPLY • link 6.3 years ago by mustafa_aljadi ▴ 10

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If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLY • link 6.3 years ago by WouterDeCoster 47k

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Thank you so much. I really appreciate your help guys. Mustafa

ADD REPLY • link 6.3 years ago by mustafa_aljadi ▴ 10

score 4 · Accepted Answer · 2018-08-15

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6.3 years ago

h.mon 35k

Use QUAST and BUSCO to evaluate the assembly.

ADD COMMENT • link 6.3 years ago by h.mon 35k

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You might want to look into the latest Quast 5.0 which includes their new LG (large genome) module that you can combine with alignment against the public reference. @h.mon the St. Petersburg folks behind Spades and Quast etc. seem to have moved to a new website http://cab.spbu.ru/

ADD REPLY • link 6.3 years ago by Carambakaracho ★ 3.3k

score 3 · Accepted Answer · 2018-08-15

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6.3 years ago

shengweima ▴ 60

New method, Assessing genome assembly quality using the LTR Assembly Index (LAI), Nucleic Acids Research

ADD COMMENT • link 6.3 years ago by shengweima ▴ 60

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It seem to be interesting, thank for the ref.

ADD REPLY • link 6.3 years ago by Beuss ▴ 140

score 2 · Accepted Answer · 2018-08-15

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6.3 years ago

btsui ▴ 300

Maybe you can compare that with the wheat ref from EMBL (ftp://ftp.ensemblgenomes.org/pub/plants/release-40/fasta/triticum_aestivum/dna/) ?

ADD COMMENT • link 6.3 years ago by btsui ▴ 300

score 2 · Accepted Answer · 2018-08-15

Do the usual : N50, assemblathon like calculations
BUSCO for evaluating completeness of gene models (+1 to @h.mon)
Align against current reference : for the contigs that do not align, are they misassemblies or collapsed duplications or proper assembled parts that the current reference failed to assemble ? Important to document.
Run a repeat finding program to identify percent repeats in the contigs and also locations - this will come in handy during further downstream analysis