From 50a9933a997e468db3343023a580308b28edc653 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 29 May 2020 08:29:31 -0500 Subject: Docs: added note about workflow runs --- doc/web/download.html | 124 +++++++++++++++++++++++++++----------------------- 1 file changed, 67 insertions(+), 57 deletions(-) (limited to 'doc/web/download.html') diff --git a/doc/web/download.html b/doc/web/download.html index 493af11..2fde013 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"> - + Download @@ -247,34 +247,44 @@ for the JavaScript code in this tag.

Table of Contents

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-

1 FASTA files

+
+

1 Workflow runs

+The last runs can be viewed here. +

+
+
+ +
+

2 FASTA files

+
+

The public sequence resource provides all uploaded sequences as FASTA files. They can be referred to from metadata individually. We also provide a single file FASTA download. @@ -282,9 +292,9 @@ also provide a single file -

2 Metadata

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+
+

3 Metadata

+

Metadata can be downloaded as Turtle RDF as a mergedmetadat.ttl which can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL @@ -305,18 +315,18 @@ graph can be downloaded from below Pangenome RDF format.

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3 Pangenome

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4 Pangenome

+

Pangenome data is made available in multiple guises. Variation graphs (VG) provide a succinct encoding of the sequences of many genomes.

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3.1 Pangenome GFA format

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4.1 Pangenome GFA format

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GFA is a standard for graphical fragment assembly and consumed by tools such as vgtools. @@ -324,9 +334,9 @@ by tools such as vgtools.

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3.2 Pangenome in ODGI format

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4.2 Pangenome in ODGI format

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ODGI is a format that supports an optimised dynamic genome/graph implementation. @@ -334,9 +344,9 @@ implementation.

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3.3 Pangenome RDF format

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4.3 Pangenome RDF format

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An RDF file that includes the sequences themselves in a variation graph can be downloaded from @@ -346,9 +356,9 @@ graph can be downloaded from

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3.4 Pangenome Browser format

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4.4 Pangenome Browser format

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The many JSON files that are named as results/1/chunk001200.bin1.schematic.json are consumed by the @@ -358,62 +368,62 @@ Pangenome browser.

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4 Log of workflow output

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5 Log of workflow output

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Including in below link is a log file of the last workflow runs.

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5 All files

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6 Planned

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7 Planned

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We are planning the add the following output (see also

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6.1 Raw sequence data

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+

7.1 Raw sequence data

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See fastq tracker and BAM tracker.

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6.2 Multiple Sequence Alignment (MSA)

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7.2 Multiple Sequence Alignment (MSA)

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See MSA tracker.

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6.3 Phylogenetic tree

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7.3 Phylogenetic tree

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See Phylo tracker.

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6.4 Protein prediction

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7.4 Protein prediction

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We aim to make protein predictions available.

@@ -422,7 +432,7 @@ We aim to make protein predictions available.
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Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-24 Sun 11:29. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-29 Fri 08:27.
-- cgit v1.2.3