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#+TITLE: Download
#+AUTHOR: Pjotr Prins
* Table of Contents :TOC:noexport:
- [[#workflow-runs][Workflow runs]]
- [[#fasta-files][FASTA files]]
- [[#metadata][Metadata]]
- [[#pangenome][Pangenome]]
- [[#pangenome-gfa-format][Pangenome GFA format]]
- [[#pangenome-in-odgi-format][Pangenome in ODGI format]]
- [[#pangenome-rdf-format][Pangenome RDF format]]
- [[#pangenome-browser-format][Pangenome Browser format]]
- [[#log-of-workflow-output][Log of workflow output]]
- [[#all-files][All files]]
- [[#planned][Planned]]
- [[#raw-sequence-data][Raw sequence data]]
- [[#multiple-sequence-alignment-msa][Multiple Sequence Alignment (MSA)]]
- [[#phylogenetic-tree][Phylogenetic tree]]
- [[#protein-prediction][Protein prediction]]
- [[#source-code][Source code]]
- [[#citing-pubseq][Citing PubSeq]]
* Workflow runs
The last runs can be viewed [[https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects][here]]. If you click on a run you can see
the workflows that ran under ~Processes~. Output (also intermediate)
is listed under ~Data collections~. All current data is listed
[[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. Note that it takes time for a run to complete and show.
* 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 [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta][FASTA download]].
* Metadata
Metadata can be downloaded as [[https://www.w3.org/TR/turtle/][Turtle RDF]] as a [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl][mergedmetadat.ttl]] which
can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL
endpoint ourselves which can be queried from
http://sparql.genenetwork.org/sparql/. Query examples can be found in
the [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org][DOCS]]
The Swiss Institute of Bioinformatics has included this data in
https://covid-19-sparql.expasy.org/ and made it part of [[https://www.uniprot.org/][Uniprot]].
An RDF file that includes the sequences themselves in a variation
graph can be downloaded from below Pangenome RDF format.
* Pangenome
Pangenome data is made available in multiple guises. Variation graphs
(VG) provide a succinct encoding of the sequences of many genomes.
** Pangenome GFA format
[[https://github.com/GFA-spec/GFA-spec][GFA]] is a standard for graphical fragment assembly and consumed
by tools such as [[https://github.com/vgteam/vg][vgtools]].
** Pangenome in ODGI format
[[https://github.com/vgteam/odgi][ODGI]] is a format that supports an optimised dynamic genome/graph
implementation.
** Pangenome RDF format
An RDF file that includes the sequences themselves in a variation
graph can be downloaded from
[[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][relabeledSeqs-dedup-relabeledSeqs-dedup.ttl.xz]].
** Pangenome Browser format
The many JSON files that are named as
[[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][results/1/chunk001200.bin1.schematic.json]] are consumed by the
Pangenome browser.
* Log of workflow output
Including in below link is a log file of the last workflow runs.
* All files
https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/
* Planned
We are planning the add the following output (see also
** Raw sequence data
See [[https://github.com/arvados/bh20-seq-resource/issues/16][fastq tracker]] and [[https://github.com/arvados/bh20-seq-resource/issues/63][BAM tracker]].
** Multiple Sequence Alignment (MSA)
See [[https://github.com/arvados/bh20-seq-resource/issues/11][MSA tracker]].
** Phylogenetic tree
See [[https://github.com/arvados/bh20-seq-resource/issues/43][Phylo tracker]].
** Protein prediction
We aim to make protein predictions available.
* Source code
All source code for this website and tooling is available
from
https://github.com/arvados/bh20-seq-resource
* Citing PubSeq
See the [[./about][FAQ]].
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