Question: How do I access genome coverage using SPADES?
0
gravatar for fhsantanna
2.9 years ago by
fhsantanna410
Brazil
fhsantanna410 wrote:

I have assembled bacterial genomes using SPADES. Now I am going to submit them to Genbank, but I need to know the coverage of each assembly. Should I provide the raw read coverage or the filtered final coverage? If the second possibility is true, how do I access these values from the SPADES log file? 

myposts coverage spades genome • 3.2k views
ADD COMMENTlink modified 15 months ago by shenwei3564.0k • written 2.9 years ago by fhsantanna410
2
gravatar for Brian Bushnell
2.9 years ago by
Walnut Creek, USA
Brian Bushnell15k wrote:

The best way to calculate coverage is by mapping, not by looking at the assembler's logs.  For example, with BBMap:

bbmap.sh in=reads.fq ref=contigs.fa covstats=covstats.txt

That will print a message like this:

Average coverage:                       278.50
Percent scaffolds with any coverage:    100.00
Percent of reference bases covered:     99.98

...in addition to creating "covstats.txt" which will list the coverage statistics for each individual scaffold.  The reads you use for mapping should be the ones you fed into Spades.

ADD COMMENTlink written 2.9 years ago by Brian Bushnell15k
1
gravatar for faisal.akbar5
15 months ago by
faisal.akbar510 wrote:

You could search "Average covergae" throughout the spades.log file.

ADD COMMENTlink written 15 months ago by faisal.akbar510
0
gravatar for shenwei356
15 months ago by
shenwei3564.0k
China
shenwei3564.0k wrote:

The contigs also have length and coverage information by which you can compute the average coverage.

$ grep '^>'  contigs.fasta | awk -F _  'BEGIN {OFS="\t"} {print $0,$4,$6}' | more
>NODE_1_length_766747_cov_499.885       766747  499.885
>NODE_2_length_581296_cov_457.579       581296  457.579
>NODE_3_length_399441_cov_525.578       399441  525.578
ADD COMMENTlink written 15 months ago by shenwei3564.0k
1

I am not 100% sure, but I think this is the k-mer coverage and not the read coverage. S.a. Confusion about the kmer coverage and http://seqanswers.com/forums/showthread.php?t=6887

ADD REPLYlink modified 13 months ago • written 13 months ago by cedric.laczny30
1

Kmer-based assemblers like Spades generally annotate contigs with kmer coverage. For read coverage, you need to map the reads against the assembly.

ADD REPLYlink written 13 months ago by Brian Bushnell15k

Thanks for your explanation.

ADD REPLYlink written 13 months ago by shenwei3564.0k
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