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Assembly of wheat genome

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
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updated by shengweima • shengweima • written by mustafa_aljadi • mustafa_aljadi

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written by WouterDeCoster WouterDeCoster

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

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written by mustafa_aljadi • mustafa_aljadi

4 answers

Use QUAST and BUSCO to evaluate the assembly.

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written by h.mon h.mon

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/

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written by Carambakaracho Carambakaracho

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

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written by shengweima • shengweima

It seem to be interesting, thank for the ref.

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written by Beuss Beuss

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

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written by btsui btsui
  1. Do the usual : N50, assemblathon like calculations
  2. BUSCO for evaluating completeness of gene models (+1 to @h.mon)
  3. 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.
  4. Run a repeat finding program to identify percent repeats in the contigs and also locations - this will come in handy during further downstream analysis
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written by shwethacm shwethacm

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