Question: Assembly of wheat genome
0
gravatar for mustafa_aljadi
14 months ago by
mustafa_aljadi0 wrote:

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 • 547 views
ADD COMMENTlink modified 14 months ago by shengweima60 • written 14 months ago by mustafa_aljadi0

Thank you so much guys for your help. Mustafa

ADD REPLYlink written 14 months ago by mustafa_aljadi0

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 REPLYlink written 14 months ago by WouterDeCoster41k

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

ADD REPLYlink written 14 months ago by mustafa_aljadi0
4
gravatar for h.mon
14 months ago by
h.mon27k
Brazil
h.mon27k wrote:

Use QUAST and BUSCO to evaluate the assembly.

ADD COMMENTlink written 14 months ago by h.mon27k
1

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 REPLYlink written 14 months ago by Carambakaracho1.7k
3
gravatar for shengweima
14 months ago by
shengweima60
China
shengweima60 wrote:

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

ADD COMMENTlink written 14 months ago by shengweima60

It seem to be interesting, thank for the ref.

ADD REPLYlink written 14 months ago by Beuss110
2
gravatar for btsui
14 months ago by
btsui290
UCSD
btsui290 wrote:

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

ADD COMMENTlink written 14 months ago by btsui290
2
gravatar for shwethacm
14 months ago by
shwethacm200
Seattle, WA
shwethacm200 wrote:
  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
ADD COMMENTlink written 14 months ago by shwethacm200
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