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schatzlab / genomescope

Fast genome analysis from unassembled short reads
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HiFi data supported ? #49

Open ptranvan opened 3 years ago

ptranvan commented 3 years ago

Hi, I have HiFi data from the low input protocol sequencing.

Ran genomescope v2 online after:

KMC/bin/kmc -k21 -t5 -m64 -ci1 -cs10000 @cat.files cat.kmcdb tmp

KMC/bin/kmc_tools transform cat.kmcdb histogram cat.kmcdb_k21.hist -cx10000

But got a weird plot:

Any clue about is happening ?

http://genomescope.org/genomescope2.0/analysis.php?code=2sNtSnC7MenouKVq7ieI

mschatz commented 3 years ago

We have successfully used HiFi data in several projects now. Unfortunately, your distribution usually indicates a quality issue, such as a mixture of individuals (or contamination) in the reads which obscures the main peaks. Do you have any other data that you could use as a baseline, perhaps Illumina data?

Good luck

Mike Schatz

On Mon, Dec 14, 2020 at 8:17 AM Patrick Tran Van notifications@github.com wrote:

Hi, I have HiFi data from the low input protocol sequencing.

Ran genomescope v2 online after:

KMC/bin/kmc -k21 -t5 -m64 -ci1 -cs10000 @cat.files cat.kmcdb tmp

KMC/bin/kmc_tools transform cat.kmcdb histogram cat.kmcdb_k21.hist -cx10000

But got a weird plot:

Any clue about is happening ?

http://genomescope.org/genomescope2.0/analysis.php?code=2sNtSnC7MenouKVq7ieI

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ptranvan commented 3 years ago

Hi @mschatz,

The Illumina sample we have is what I described in:

https://github.com/schatzlab/genomescope/issues/48

mschatz commented 3 years ago

Right -- these are markedly different so unfortunately there is likely a contamination or other quality issue with your HiFi data

Good luck

Mike

On Tue, Dec 15, 2020 at 6:06 AM Patrick Tran Van notifications@github.com wrote:

Hi @mschatz https://github.com/mschatz,

The Illumina sample we have is what I described in:

48 https://github.com/schatzlab/genomescope/issues/48

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