repository for materials to do with the VGP phase 1 data freeze, analyses, and publication
- 2025-05-10 - added taxId and taxon strings from NCBI for taxonomy analysis in two files: primary.taxon.metaData.tsv and secondary.taxon.metaData.tsv
- 2025-05-08 - replaced primary/otherChordates/GCF_010993605.1 with updated sea lamprey assembly: primary/otherChordates/GCA_048934315.1, moved GCF_010993605.1 to secondary, renamed GCF_009914755.1 to GCA_009914755.4 (T2T-CHM13v2.0)
- 2025-04-29 - assembly list verified, correctly repeat masked sequences now available at: UCSC hgdownload
- 2025-04-21 - finishing the complete RepeatMasking of all the assemblies
- 2025-04-11 - Checking, verifying the assembly listings
- primary the best assembly (haplotype) for the species, to be used in the primary multiple-alignment
- seconday the alternate haplotype that corresponds to the primary assembly for this species.
- primary: 581 ==
cut -f16 VGPPhase1-freeze-1.0.tsv | grep -c GC - primary with RefSeq version: 246 ==
cut -f16,17 VGPPhase1-freeze-1.0.tsv | grep -c GCF - secondary: 264 ==
cut -f22 VGPPhase1-freeze-1.0.tsv | tr ',' '\n' | tr -d ' ' | grep GC | wc -l
There are 246 primary assemblies that have both a GenBank and a RefSeq released version from NCBI. There are four files here to summarize the differences between the two assemblies. The differences are always because one or the other assembly will have a chrMT sequence that is not in the other.
- 47 identical assemblies, GenBank and RefSeq are identical in all sequences
- 44 RefSeq assemblies have an added chrMT sequence from the GenBank assembly
- 124 RefSeq has removed the chrMT sequence that was in the GenBank assembly
- 31 assemblies have the same count of sequences, but each one has a unique chrMT sequence
- common names need to be coordinated between UCSC names and the names from the spreadsheet. We have a lot of different names right now, in general Erich's spreadsheet names will most likely prevail.