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Added a section about the Arima mapping pipeline #70

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Jun 7, 2024
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Added a section about the Arima mapping pipeline #70

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13 changes: 12 additions & 1 deletion markdown/resources/tools.md
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Expand Up @@ -56,10 +56,21 @@ Pretext is a suite of tools used to curate the chromosome level structure of lon

- [PretextSnapshot](https://github.com/sanger-tol/PretextSnapshot) - Extracts Hi-C contact map images from Pretext map files.

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

<br/>

## AGP / TPF Utilities

Nucleotide coodinates (other than the start or end of contigs) in AGP files produced by [PretextView](https://github.com/sanger-tol/PretextView) are only accurate to the number of bases spanned by each pixel in its map file. The `pretext-to-tpf` command of [AGP / TPF Utilites](https://github.com/sanger-tol/agp-tpf-utils/) uses the orginal, unedited assembly to correct the coordinates of the assembly contigs. It also uses tags from PretextView to label chromosomes, and to separate haplotypes, haplotigs and contaminants.

<br/>

## 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>.

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