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Added GenomeSize.xml for whole chr22 #2188

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Merged
Schmytzi merged 3 commits into from
Jul 30, 2026
Merged

Added GenomeSize.xml for whole chr22 #2188

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8e87095
Added GenomeSize.xml for whole chr22
Schmytzi Jul 29, 2026
bd12f97
Added new file to README
Schmytzi Jul 29, 2026
946727e
Appeasing formatter
Schmytzi Jul 30, 2026
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15 changes: 15 additions & 0 deletions data/genomics/homo_sapiens/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -228,6 +228,21 @@ cat << EOF > GenomeSize.xml
EOF
```

Similarly, the GenomeSize.xml index for the entirety of chr22 (`homo_sapiens/genome/chr22/sequence/GenomeSize.xml`) was created accordingly:

```bash
stripped_seq=$(mktemp)
tail -n +2 hg38.chr22.fasta | tr -d '\n' > $stripped_seq
length=$(wc -c $stripped_seq | cut -f 1 -d ' ' )
md5=$(md5sum $stripped_seq | cut -f 1 -d ' ' )

cat << EOF > GenomeSize.xml
<sequenceSizes genomeName="Homo Sapiens (NCBI GRCh38)">
<chromosome fileName="genome.fa" contigName="chr22" totalBases="${length}" build="GRCh38" isCircular="false" md5="${md5}" ploidy="2" species="Homo_sapiens" knownBases="${length}" type="Autosome" />
</sequenceSizes>
EOF
```

### Genome map

There is multiple type of genetic map depending on the softwares.
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4 changes: 4 additions & 0 deletions data/genomics/homo_sapiens/genome/chr22/sequence/GenomeSize.xml
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<sequenceSizes genomeName="Homo Sapiens (NCBI GRCh38)">
<chromosome fileName="genome.fa" contigName="chr22" totalBases="50818468" build="GRCh38" isCircular="false" md5="ac37ec46683600f808cdd41eac1d55cd" ploidy="2" species="Homo_sapiens" knownBases="50818468" type="Autosome" />
</sequenceSizes>