https://github.com/mojaveazure/utilities

A repository full of bioinformatics-related utilities
https://github.com/mojaveazure/utilities

Last synced: 18 days ago
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A repository full of bioinformatics-related utilities

• Host: GitHub
• URL: https://github.com/mojaveazure/utilities
• Owner: mojaveazure
• Created: 2016-07-12T13:56:22.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-03-21T22:16:38.000Z (almost 8 years ago)
• Last Synced: 2024-10-15T09:11:16.910Z (2 months ago)
• Language: Python
• Size: 43.9 KB
• Stars: 1
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Utilities

A repository full of bioinformatics-related utilities

To download, install Git on your computer and run the following command:

```bash

git clone --recursive https://github.com/mojaveazure/Utilities.git

```

To update this repository, run the following commands:

```bash

git pull

git submodule update --remote --merge

```

- `SAM_to_SNP.py`: A Python 3 script that calculates exact SNP position using an Illumina lookup table, SAM file for contextual sequences, and reference genome

- `fakeHeader.sh`: A BASH shell script to add the '@HD' header to a SAM or BAM file

- `getCoverage.sh`: A BASH shell script to calculate the coverage from a BEDTools coverage histogram

- `idxSummarize.sh`: A BASH shell script that creates a single file summarizing the results from SAMTools idxstats

- `subsample.sh`: A BASH shell script that randomly subsamples a FastQ file

- `makeFOF.R`: an R script to make a FOF for Consed from a list of regions and reference fasta