mojaveazure / Utilities

A repository full of bioinformatics-related utilities

Utilities

A repository full of bioinformatics-related utilities

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

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

To update this repository, run the following commands:

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