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jgrg authored and muffato committed Jun 7, 2024
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## Arima mapping pipeline

Arima Genomics provides us the kits used to do genome-wide Hi-C for genome assembly.
They have released some [open source scripts](https://github.com/ArimaGenomics/mapping_pipeline) to aid mapping the reads onto a genome assembly.
We have slightly modified the scripts to support the CRAM files we get from Sanger's sequencing teams.
The code is on our fork of the repostitory on GitHub: <https://github.com/sanger-tol/arima_mapping_pipeline>.
Arima Genomics, who supply the kits we use to produce Hi-C data for genome assembly,
have released [open source scripts](https://github.com/ArimaGenomics/mapping_pipeline) which aid mapping the reads to a genome assembly.
We have modified them to support the CRAM files produced by Sanger's sequencing teams,
and have made these changes are available in our [fork of the repository on GitHub](https://github.com/sanger-tol/arima_mapping_pipeline).

**Pipelines:** [curationpretext](/curationpretext) | [genomeassembly](/genomeassembly) | [treeval](/treeval)

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