PacBio data on GIAB FTP for AJ Trio and NA12878

[Justin Zook]

We are pleased to announce two new PacBio datasets that are now on the GIAB FTP site:

1. In a collaboration between NIST and Mt. Sinai School of Medicine, we have completed PacBio sequencing of the Ashkenazim Jewish trio that is a candidate NIST Reference Material.  Raw data is on the FTP site, with ~69x coverage of the son, 32x on the father, and 30x on the mother.  ~90% of the data for each genome is from P6-C4 chemistry and the remaining from P5-C3.  The N50 read length is ~11kb.  All of these data are public without embargo, but we encourage you to participate in our GIAB Analysis Group if you are interested in analyzing these data.  The data and a readme with further information are available at:

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/pacbio_AJTrio/HG002_HG003_HG004

Note that we plan to put the h5 files in the SRA and in the data directory as well in the coming weeks, and the analysis group is working on mapping these data and bam files will be uploaded as well.

2. Mt. Sinai School of Medicine has also kindly uploaded their PacBio sequencing for NA12878 to our GIAB ftp.  They have uploaded the raw h5 files as well as a vcf containing SV calls, error-corrected reads, and a bam file.  Look for their paper in Nature Methods to be published soon!  Their uploaded files and a readme with more information are at:

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/NA12878_PacBio_MtSinai

Cheers,

Justin Zook

[Adam Phillippy]

Thanks, Justin!

Sergey and I plan to assemble the PacBio trio data. We should have assemblies of the parents done by the end of this month and the son sometime in June. We will distribute these to the group as soon as we have them.

Best,

-Adam

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[michael.schatz]

Other than Adam's note about assembling these, has anyone started to work with these data? Im interested to look at them for SV calling with my postdoc Fritz but dont want to duplicate efforts.

Thank you

Mike

On Monday, May 18, 2015 at 4:52:41 PM UTC-4, Adam Phillippy wrote:

Thanks, Justin!

Sergey and I plan to assemble the PacBio trio data. We should have assemblies of the parents done by the end of this month and the son sometime in June. We will distribute these to the group as soon as we have them.

Best,

-Adam

On Mon, May 18, 2015 at 4:25 PM, Justin Zook <justi...@gmail.com> wrote:

We are pleased to announce two new PacBio datasets that are now on the GIAB FTP site:

1. In a collaboration between NIST and Mt. Sinai School of Medicine, we have completed PacBio sequencing of the Ashkenazim Jewish trio that is a candidate NIST Reference Material.  Raw data is on the FTP site, with ~69x coverage of the son, 32x on the father, and 30x on the mother.  ~90% of the data for each genome is from P6-C4 chemistry and the remaining from P5-C3.  The N50 read length is ~11kb.  All of these data are public without embargo, but we encourage you to participate in our GIAB Analysis Group if you are interested in analyzing these data.  The data and a readme with further information are available at:

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/pacbio_AJTrio/HG002_HG003_HG004

Note that we plan to put the h5 files in the SRA and in the data directory as well in the coming weeks, and the analysis group is working on mapping these data and bam files will be uploaded as well.

2. Mt. Sinai School of Medicine has also kindly uploaded their PacBio sequencing for NA12878 to our GIAB ftp.  They have uploaded the raw h5 files as well as a vcf containing SV calls, error-corrected reads, and a bam file.  Look for their paper in Nature Methods to be published soon!  Their uploaded files and a readme with more information are at:

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/NA12878_PacBio_MtSinai

Cheers,

Justin Zook

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[Andrew Carroll]

We at DNAnexus are working with them for structural variant calling and genome assembly in various contexts. I suspect our efforts are complementary and likely not overlapping at this current point (adding in Brett Hannigan  and George Asimenos who are involved in the process).

We'd be happy to coordinate if you're interested.

On Tue, Jun 2, 2015 at 10:21 PM, michael.schatz <michael...@gmail.com> wrote:

Other than Adam's note about assembling these, has anyone started to work with these data? Im interested to look at them for SV calling with my postdoc Fritz but dont want to duplicate efforts.

Thank you

Mike

On Monday, May 18, 2015 at 4:52:41 PM UTC-4, Adam Phillippy wrote:

Thanks, Justin!

Sergey and I plan to assemble the PacBio trio data. We should have assemblies of the parents done by the end of this month and the son sometime in June. We will distribute these to the group as soon as we have them.

Best,

-Adam

On Mon, May 18, 2015 at 4:25 PM, Justin Zook <justi...@gmail.com> wrote:

We are pleased to announce two new PacBio datasets that are now on the GIAB FTP site:

1. In a collaboration between NIST and Mt. Sinai School of Medicine, we have completed PacBio sequencing of the Ashkenazim Jewish trio that is a candidate NIST Reference Material.  Raw data is on the FTP site, with ~69x coverage of the son, 32x on the father, and 30x on the mother.  ~90% of the data for each genome is from P6-C4 chemistry and the remaining from P5-C3.  The N50 read length is ~11kb.  All of these data are public without embargo, but we encourage you to participate in our GIAB Analysis Group if you are interested in analyzing these data.  The data and a readme with further information are available at:

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/pacbio_AJTrio/HG002_HG003_HG004

Note that we plan to put the h5 files in the SRA and in the data directory as well in the coming weeks, and the analysis group is working on mapping these data and bam files will be uploaded as well.

2. Mt. Sinai School of Medicine has also kindly uploaded their PacBio sequencing for NA12878 to our GIAB ftp.  They have uploaded the raw h5 files as well as a vcf containing SV calls, error-corrected reads, and a bam file.  Look for their paper in Nature Methods to be published soon!  Their uploaded files and a readme with more information are at:

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/NA12878_PacBio_MtSinai

Cheers,

Justin Zook

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[Michael Schatz]

Actually we have been exploring SV detection from the error corrected reads as well as raw reads. Do you have a FALCON run complete already? That would save us a considerable about of time.

Thank you,

Mike

[Bashir, Ali]

Hi Mike,

I have a falcon assembly ru complete for the child - I will try to upload that today.  Note, it has not been quiver corrected yet.

-Ali

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[Robert Sebra Gmail]

Hi Ali, Mike et al.

I’ll try and get the Quiver correction done ASAP and then get that to you, Ali.

B

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[Adam Phillippy]

Hey Mike,

I was planning on looking at SVs as well, but starting from the assemblies. I believe we have both parents assembled and Quivered, and the child should be done soon. Will post those CA assemblies for the group shortly.

-Adam

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[Lina M. Solis Castillero]

Dear Justin,

How can I access to the SNPs database do you already have for the
RM-8398 I just bought, I can't find it.
I really appreciate ypour help,

Thanks!


Justin Zook <justi...@gmail.com> escribió:

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Saludos cordiales,

Lina M. Solis Castillero. TM MSc.
Master en Genetica y Biologia Molecular.
Directora General
Laboratorio Clinico Genetix, S.A.
La Alameda, Calle Makario 3 de Chipre,
Edif. Plaza San Marcos # 1, Local 6 PB.
www.genetix.com.pa
Tel. (507) 260-2990 (507)260-2999.

Ayúdenos a servirle mejor, por favor responda la encuesta de
satisfacción que encontrará en el siguiente link:
http://www.surveymonkey.com/s/CY6ZYDP
Gracias!

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[michael.schatz]

Is the readme available for the PacBio AJ Trio data? There is a long list of directories here, but it is not clear which data are good or bad (with _new versus without?):

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/pacbio_AJTrio/HG002_HG003_HG004

Thank you!

Mike

[Justin Zook]

Hi Mike,

Yes, there's a readme in the directory just above that: ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/pacbio_AJTrio 

Cheers,

Justin

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[Michael Schatz]

Thanks! Sorry I missed it, it was so cleverly hidden :)

Mike 

[Justin Zook]

Dear Lina,

The locations of the high-confidence vcf and bed files will be listed in the Report of Investigation you'll get with the DNA and it is also online here: 

http://tinyurl.com/giabpilotreport 

Cheers,

Justin

[Lina M. Solis Castillero]

Dear Justin,

Thank you very much!


Justin Zook <justi...@gmail.com> escribió: