COVID-19 PubSeq is a free and open online bioinformatics public sequence resource with - on-the-fly analysis of sequenced SARS-CoV-2 + on-the-fly analysis of + sequenced SARS-CoV-2 samples that allows for a quick turnaround in identification of new virus strains. PubSeq allows anyone to upload sequence material in the form of FASTA or FASTQ files with accompanying metadata - through the web interface or REST API. For more information see the FAQ!. + through the web interface + or REST API. For more + information see the FAQ!.
+
Make your sequence data FAIR. Upload @@ -40,10 +48,16 @@ a Creative Commons license You can take the published (GFA/RDF/FASTA) data and store it in a triple - store for further processing. Clinical data can + store for further processing. + Clinical data can be stored securely at REDCap.
+
+ + We give special attention to workflows for the Oxford Nanopore - see pubmed - because it offers an affordable platform that is great + for SARS-CoV-2 sequencing. +
Note that form fields contain
web ontology
@@ -55,10 +69,6 @@
-
PubSeq, the public sequence resource, aims to provide a generic and
@@ -322,8 +323,8 @@ follow.
We presented at the BOSC 2020 Have a look at the video (alternative
@@ -332,8 +333,8 @@ link) and the
-
The public sequence resource is an initiative by bioinformatics and
@@ -354,8 +355,8 @@ wrangling experts. Thank you everyone!
The short version is that we use state-of-the-art practices in
@@ -378,8 +379,8 @@ such as GISAID.
Funny question. There are only good reasons to upload your data here
@@ -433,8 +434,8 @@ for bulk uploads!
On uploading a sequence with metadata it will automatically be
@@ -445,8 +446,8 @@ using workflows from the High Performance Open Biology Lab defined
The Swiss Institute of Bioinformatics has included this data in
@@ -464,8 +465,8 @@ for monitoring, protein prediction and drug development.
You can contribute by submitting sequences, updating metadata, submit
@@ -477,8 +478,8 @@ point.
All data is published under a Creative Commons 4.0 attribution license
@@ -488,8 +489,8 @@ data and store it for further processing.
Absolutely. Free software allows for fully reproducible pipelines. You
@@ -498,8 +499,8 @@ can take our workflows and data and run it elsewhere!
We are preparing raw sequence data pipelines (fastq and BAM). The
@@ -514,8 +515,8 @@ assembly variations into consideration. This is all work in progress.
See the http://covid19.genenetwork.org/blog!
@@ -523,8 +524,8 @@ See the http://covid19.genenetwork
Workflows are on github and can be modified. See also the BLOG
@@ -533,8 +534,8 @@ Workflows are on
-
Go to our source code repositories, fork/clone the repository, change
@@ -544,8 +545,8 @@ many PRs we already merged.
Restrictive data licenses are hampering data sharing and reproducible
@@ -561,8 +562,8 @@ In all honesty: we prefer both data and software to be free.
We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly.
@@ -574,8 +575,8 @@ We are also writing tools to generate VCF files directly from the pangenome.
A public sequence resource is about public data. Metadata can refer to
@@ -586,8 +587,8 @@ plan to combine identifiers with clinical data stored securely at
We are planning to remove reads that match the human reference.
@@ -595,8 +596,8 @@ We are planning to remove reads that match the human reference.
To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future.
@@ -605,8 +606,8 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to
We use a gitter channel you can join. See also contact.
@@ -614,10 +615,26 @@ We use a
-
+We have two publications in the works. Until we have a DOI please cite
+PubSeq in the following way:
+
+We made use of the COVID-19 public sequence (PubSeq) resources hosted
+at http://covid19.genenetwork.org/.
+
The main sponsors are listed in the footer. In addition to the time
generously donated by many contributors we also acknowledge Amazon AWS
for donating COVID-19 related compute time.
@@ -626,7 +643,7 @@ for donating COVID-19 related compute time.
The last runs can be viewed here. If you click on a run you can see
@@ -285,8 +286,8 @@ is listed under
The public sequence resource provides all uploaded sequences as
@@ -296,8 +297,8 @@ also provide a single file
-
Metadata can be downloaded as Turtle RDF as a mergedmetadat.ttl which
@@ -319,8 +320,8 @@ graph can be downloaded from below Pangenome RDF format.
Pangenome data is made available in multiple guises. Variation graphs
@@ -328,8 +329,8 @@ Pangenome data is made available in multiple guises. Variation graphs
ODGI is a format that supports an optimised dynamic genome/graph
@@ -348,8 +349,8 @@ implementation.
An RDF file that includes the sequences themselves in a variation
@@ -360,8 +361,8 @@ graph can be downloaded from
The many JSON files that are named as
@@ -372,8 +373,8 @@ Pangenome browser.
Including in below link is a log file of the last workflow runs.
@@ -381,8 +382,8 @@ Including in below link is a log file of the last workflow runs.
https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/
@@ -390,16 +391,16 @@ Including in below link is a log file of the last workflow runs.
We are planning the add the following output (see also
See fastq tracker and BAM tracker.
@@ -407,8 +408,8 @@ See fastq track
See MSA tracker.
@@ -416,8 +417,8 @@ See MSA tracker
See Phylo tracker.
@@ -425,8 +426,8 @@ See Phylo track
We aim to make protein predictions available.
@@ -435,8 +436,8 @@ We aim to make protein predictions available.
All source code for this website and tooling is available
@@ -445,9 +446,18 @@ from
+See the FAQ.
+Table of Contents
-
-
-1 What is the 'public sequence resource' about?
+
+
-1 What is the 'public sequence resource' about?
-2 Presentations
+
+2 Presentations
3 Who created the public sequence resource?
+
+
-3 Who created the public sequence resource?
-4 How does the public sequence resource compare to other data resources?
+
+
-4 How does the public sequence resource compare to other data resources?
-5 Why should I upload my data here?
+
+
-5 Why should I upload my data here?
-6 Why should I not upload by data here?
+
+
-6 Why should I not upload by data here?
-7 How does the public sequence resource work?
+
+
-7 How does the public sequence resource work?
-8 Who uses the public sequence resource?
+
+
-8 Who uses the public sequence resource?
-9 How can I contribute?
+
+
-9 How can I contribute?
-10 Is this about open data?
+
+
-10 Is this about open data?
-11 Is this about free software?
+
+
-11 Is this about free software?
-12 How do I upload raw data?
+
+
-12 How do I upload raw data?
-13 How do I change metadata?
+
+
-13 How do I change metadata?
-14 How do I change the work flows?
+
+14 How do I change the work flows?
15 How do I change the source code?
+
+
-15 How do I change the source code?
-16 Should I choose CC-BY or CC0?
+
+
-16 Should I choose CC-BY or CC0?
-17 Are there also variant in the RDF databases? *
+
+
-17 Are there also variant in the RDF databases?
-18 How do I deal with private data and privacy?
+
+
-18 How do I deal with private data and privacy?
-19 Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *
+
+
-19 Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *
-20 Does PubSeq support only SARS-CoV-2 data? *
+
+20 Does PubSeq support only SARS-CoV-2 data?
-
-21 How do I communicate with you?
+
+21 How do I communicate with you?
-22 Who are the sponsors?
+
+
+
+
+22 Citing PubSeq
+
+
23 Who are the sponsors?
+
+
-
diff --git a/doc/web/about.org b/doc/web/about.org
index 1b7bda1..d8d7f73 100644
--- a/doc/web/about.org
+++ b/doc/web/about.org
@@ -18,11 +18,12 @@
- [[#how-do-i-change-the-work-flows][How do I change the work flows?]]
- [[#how-do-i-change-the-source-code][How do I change the source code?]]
- [[#should-i-choose-cc-by-or-cc0][Should I choose CC-BY or CC0?]]
- - [[#are-there-also-variant-in-the-rdf-databases-][Are there also variant in the RDF databases? *]]
+ - [[#are-there-also-variant-in-the-rdf-databases][Are there also variant in the RDF databases?]]
- [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]]
- [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq-][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *]]
- - [[#does-pubseq-support-only-sars-cov-2-data-][Does PubSeq support only SARS-CoV-2 data? *]]
+ - [[#does-pubseq-support-only-sars-cov-2-data][Does PubSeq support only SARS-CoV-2 data?]]
- [[#how-do-i-communicate-with-you][How do I communicate with you?]]
+ - [[#citing-pubseq][Citing PubSeq]]
- [[#who-are-the-sponsors][Who are the sponsors?]]
* What is the 'public sequence resource' about?
@@ -209,7 +210,7 @@ because we know people like the attribution clause.
In all honesty: we prefer both data and software to be free.
-* Are there also variant in the RDF databases? *
+* Are there also variant in the RDF databases?
We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly.
@@ -226,7 +227,7 @@ plan to combine identifiers with clinical data stored securely at
We are planning to remove reads that match the human reference.
-* Does PubSeq support only SARS-CoV-2 data? *
+* Does PubSeq support only SARS-CoV-2 data?
To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future.
@@ -235,6 +236,15 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to
We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. See also [[./contact][contact]].
+* Citing PubSeq
+
+We have two publications in the works. Until we have a DOI please cite
+PubSeq in the following way:
+
+We made use of the COVID-19 public sequence (PubSeq) resources hosted
+at http://covid19.genenetwork.org/.
+
+
* Who are the sponsors?
The main sponsors are listed in the footer. In addition to the time
diff --git a/doc/web/download.html b/doc/web/download.html
index 1d196a0..998c87b 100644
--- a/doc/web/download.html
+++ b/doc/web/download.html
@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-23 Sun 04:26.
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-24 Mon 03:12.
Table of Contents
-1 Workflow runs
+
+
-1 Workflow runs
Data collections. All current data is listed
-2 FASTA files
+
+2 FASTA files
3 Metadata
+
+
-3 Metadata
-4 Pangenome
+
+4 Pangenome
-
-4.1 Pangenome GFA format
+
+
-4.1 Pangenome GFA format
-4.2 Pangenome in ODGI format
+
+
-4.2 Pangenome in ODGI format
-4.3 Pangenome RDF format
+
+4.3 Pangenome RDF format
-
-4.4 Pangenome Browser format
+
+
-4.4 Pangenome Browser format
-5 Log of workflow output
+
+
-5 Log of workflow output
-6 All files
+
+
-6 All files
-7 Planned
+
+7 Planned
-
-7.1 Raw sequence data
+
+
-7.1 Raw sequence data
-7.2 Multiple Sequence Alignment (MSA)
+
+
-7.2 Multiple Sequence Alignment (MSA)
-7.3 Phylogenetic tree
+
+
-7.3 Phylogenetic tree
-7.4 Protein prediction
+
+
-7.4 Protein prediction
-
8 Source code
+
+
+
+8 Source code
+
9 Citing PubSeq
+
+
+
-
diff --git a/doc/web/download.org b/doc/web/download.org
index 7614c60..a3f1949 100644
--- a/doc/web/download.org
+++ b/doc/web/download.org
@@ -18,6 +18,7 @@
- [[#phylogenetic-tree][Phylogenetic tree]]
- [[#protein-prediction][Protein prediction]]
- [[#source-code][Source code]]
+ - [[#citing-pubseq][Citing PubSeq]]
* Workflow runs
@@ -107,3 +108,7 @@ We aim to make protein predictions available.
All source code for this website and tooling is available
from
https://github.com/arvados/bh20-seq-resource
+
+* Citing PubSeq
+
+See the [[./about][FAQ]].
--
cgit v1.2.3
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-06-12 Fri 04:41.
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-24 Mon 03:07.