Question: Assembly of wheat genome
0
gravatar for mustafa_aljadi
8 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 • 451 views
ADD COMMENTlink modified 8 months ago by shengweima60 • written 8 months ago by mustafa_aljadi0

Thank you so much guys for your help. Mustafa

ADD REPLYlink written 8 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 8 months ago by WouterDeCoster38k

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

ADD REPLYlink written 8 months ago by mustafa_aljadi0
4
gravatar for h.mon
8 months ago by
h.mon24k
Brazil
h.mon24k wrote:

Use QUAST and BUSCO to evaluate the assembly.

ADD COMMENTlink written 8 months ago by h.mon24k
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 8 months ago by Carambakaracho960
3
gravatar for shengweima
8 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 8 months ago by shengweima60

It seem to be interesting, thank for the ref.

ADD REPLYlink written 8 months ago by Beuss100
2
gravatar for btsui
8 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 8 months ago by btsui290
2
gravatar for shwethacm
8 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 8 months ago by shwethacm200
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