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2025
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| Online Access: | https://doi.org/10.5281/zenodo.14866638 |
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| _version_ | 1866901600828653568 |
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| author | Turner, Tychele |
| author_facet | Turner, Tychele |
| contents | <p>EGP: El genoma pequeño - analysis workflow for "the little genome"</p> <p>Creator and Developer: Tychele N. Turner, Ph.D.</p> <p>The mitochondrial workflows in this github have a few purposes. First is to get a high quality mitochondrial genome out of an Illumina sequencing bam or cram file (this workflow assumes this bam/cram was initially mapped to a reference using BWA MEM). Second is to get a representative fasta for the mitochondrial genome and to use Mitomaster to determine its haplogroup. Third is to collect variants from the mitochondrial genome including those which meet some minimum threshold for being a heteroplasmic variant. Fourth is to generate an estimate of mitochondrial genome copy number. Finally, it generates a world map with your sample(s) mapped to the location where their haplogroup is thought to have been derived in the world. To generate coordinates, I approximated based on looking at the following map: <a href="https://www.mitomap.org/foswiki/pub/MITOMAP/MitomapFigures/WorldMigrations2012.pdf" rel="nofollow">https://www.mitomap.org/foswiki/pub/MITOMAP/MitomapFigures/WorldMigrations2012.pdf</a>.</p> <p>We highly suggest some other analyses for family-based studies such as taking all of the fastas and generating a multi-sequence alignment and tree (they are not currently implemented in this github). The workflows in this github run in ~ 2 minutes per sample.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_14866638 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | EGP Turner, Tychele <p>EGP: El genoma pequeño - analysis workflow for "the little genome"</p> <p>Creator and Developer: Tychele N. Turner, Ph.D.</p> <p>The mitochondrial workflows in this github have a few purposes. First is to get a high quality mitochondrial genome out of an Illumina sequencing bam or cram file (this workflow assumes this bam/cram was initially mapped to a reference using BWA MEM). Second is to get a representative fasta for the mitochondrial genome and to use Mitomaster to determine its haplogroup. Third is to collect variants from the mitochondrial genome including those which meet some minimum threshold for being a heteroplasmic variant. Fourth is to generate an estimate of mitochondrial genome copy number. Finally, it generates a world map with your sample(s) mapped to the location where their haplogroup is thought to have been derived in the world. To generate coordinates, I approximated based on looking at the following map: <a href="https://www.mitomap.org/foswiki/pub/MITOMAP/MitomapFigures/WorldMigrations2012.pdf" rel="nofollow">https://www.mitomap.org/foswiki/pub/MITOMAP/MitomapFigures/WorldMigrations2012.pdf</a>.</p> <p>We highly suggest some other analyses for family-based studies such as taking all of the fastas and generating a multi-sequence alignment and tree (they are not currently implemented in this github). The workflows in this github run in ~ 2 minutes per sample.</p> |
| title | EGP |
| url | https://doi.org/10.5281/zenodo.14866638 |