Update Zika notes

nextstrain · Jan 9, 2017 · e59e26f · e59e26f
1 parent 3a5f767
commit e59e26f
Showing 1 changed file with 41 additions and 36 deletions.
diff --git a/ZIKA.md b/ZIKA.md
@@ -1,16 +1,7 @@
 # ZIKA Pipeline Notes
 
-## Upload documents to VDB
-1. Download sequences from [VIPR](https://www.viprbrc.org/brc/vipr_genome_search.spg?method=ShowCleanSearch&decorator=flavi_zika)
-  * Select year >= 2013 and genome length >= 5000
-  * Download as Genome Fasta
-  * Set Custom Format Fields to 0: GenBank Accession, 1: Strain Name, 2: Segment, 3: Date, 4: Host, 5: Country, 6: Subtype, 7: Virus Species
-2. Move downloaded sequences to `fauna/data`
-3. Upload to vdb database
-  * `python vdb/zika_upload.py -db vdb -v zika --source vipr --locus genome --fname GenomeFastaResults.fasta`
-
-
 ## Update documents in VDB
+
 * Update citation fields
   * `python vdb/zika_update.py -db vdb -v zika --update_citations`
   * updates `authors`, `title` and `url` fields from genbank files
@@ -21,42 +12,56 @@
   * Updates `division`, `country`, `region`, `latitude`, `longitude` fields
 
 ## Download documents from VDB
+
 * `python vdb/zika_download.py -db vdb -v zika --fstem zika`
 
-# ZIBRA sequences
+## Upload
+
+### [ViPR sequences](ttps://www.viprbrc.org/brc/vipr_genome_search.spg?method=ShowCleanSearch&decorator=flavi_zika)
+
+1. Download sequences
+  * Select year >= 2013 and genome length >= 5000
+  * Download as Genome Fasta
+  * Set Custom Format Fields to 0: GenBank Accession, 1: Strain Name, 2: Segment, 3: Date, 4: Host, 5: Country, 6: Subtype, 7: Virus Species
+2. Move downloaded sequences to `fauna/data`
+3. Upload to vdb database
+  * `python vdb/zika_upload.py -db vdb -v zika --source vipr --locus genome --fname GenomeFastaResults.fasta`
+
+### [ZiBRA sequences](https://github.com/zibraproject/zibraproject.github.io/tree/master/data/consensus)
 
-## Upload documents to VDB
-Regex replace: `^>([^|]+)\|([^|]+)\|([^|]+)\|([^|]+)\|(\S+) .+`
-With: `>\1|\1|\5|brazil|\4|\3`
-then
-Regex replace: `^>([^|]+)\|\d.+`
-With: `>\1|\1|XXXX-XX-XX|brazil`
-Upload with: `python vdb/zibra_upload.py -db vdb -v zika --source zibra --locus genome --authors "Zika in Brazil Real-time Analysis Consortium" --fname BRA_ZIBRA_Good.fasta`
-And: `python vdb/zibra_upload.py -db vdb -v zika --source zibra --locus genome --authors "Zika in Brazil Real-time Analysis Consortium" --fname BRA_ZIBRA_Partial.fasta`
+* Replace `^>([^|]+)\|([^|]+)\|([^|]+)\|([^|]+)\|(\S+) .+` with `>\1|\1|\5|brazil|\4|\3`
+* Replace `^>([^|]+)\|\d.+` with `>\1|\1|XXXX-XX-XX|brazil`
 
-# Andersen sequences
+Upload with:
+
+    python vdb/zibra_upload.py -db vdb -v zika --source zibra --locus genome --authors "Zika in Brazil Real-time Analysis Consortium" --fname BRA_ZIBRA_Good.fasta
+    python vdb/zibra_upload.py -db vdb -v zika --source zibra --locus genome --authors "Zika in Brazil Real-time Analysis Consortium" --fname BRA_ZIBRA_Partial.fasta
 
-## Upload documents to VDB
-Regex replace: `^>([^|]+)\|XX\|`
-With: `>\1|\1|`
-Upload with: `python vdb/zibra_upload.py -db vdb -v zika --source andersen --locus genome --authors "Grubaugh et al" --fname andersen.fasta`
+### [Scripps sequences](https://github.com/andersen-lab/zika-florida/tree/master/consensus_sequences)
 
-# Broad sequences
+* Replace: `^>([^|]+)\|XX\|` with `>\1|\1|`
+
+Upload with:
 
-## Upload documents to VDB
-Upload with: `python vdb/zika_upload.py -db vdb -v zika --source broad --locus genome --authors "Broad Viral Genomics Group" --fname ZIKV_BROAD_2016-10.fasta`
+    python vdb/zibra_upload.py -db vdb -v zika --source andersen --locus genome --authors "Grubaugh et al" --fname andersen.fasta
 
-# USAMRIID sequences
+### [Broad sequences](http://virological.org/t/33-zika-virus-genomes-sequenced-from-patient-and-pooled-mosquito-samples/372)
+
+Upload with:
+
+    python vdb/zika_upload.py -db vdb -v zika --source broad --locus genome --authors "Broad Viral Genomics Group" --fname ZIKV_BROAD_2016-10.fasta
+
+### [USAMRIID sequences](https://github.com/jtladner/ZIKA_Florida/tree/master/sequences)
+
+* Replace: `^>([^_]+)_[^_]+_[^_]+_(\S+)` with `>\1|\1|\2|human|usa|florida|florida`
+
+Upload with:
 
-## Upload documents to VDB
-Regex replace: `^>([^_]+)_[^_]+_[^_]+_(\S+)`
-With: `>\1|\1|\2|human|usa|florida|florida`
-Upload with: `python vdb/zibra_upload.py -db vdb -v zika --source usamriid --locus genome --authors "Ladner et al" --fname RIID_ZIKV_FL_10-27-16.fasta`
+    python vdb/zibra_upload.py -db vdb -v zika --source usamriid --locus genome --authors "Ladner et al" --fname RIID_ZIKV_FL_10-27-16.fasta
 
-# FH sequences
+### [Fred Hutch sequences](https://github.com/blab/zika-seq/tree/master/consensus-genomes)
 
-## Upload documents to VDB
 Upload with:
 
-* `python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname ZIKA_good.fasta`
-* `python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname ZIKA_partial.fasta`
+    python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname ZIKA_good.fasta
+    python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname ZIKA_partial.fasta