README.md

random-scripts

Small scripts for semi-common tasks.

For subsampling sequencing data:

bootstrap_samtofastq.py

This script will take a .sam file as input, and return a .fastq or .fastq.gz that approximately contains a specified number of reads. It also contains an option for pre-filtering the input for full-length reads.

Example

python bootstrap_samtofastq.py input-file.sam --filter --out output-file.fastq.gz --reads 10000 20000

This command would create 3 new files:

• input-file_fullength.sam - containing only full-length alignments
• output-file_10000.fastq.gz - containing approximately 10,000 reads
• output-file_20000.fastq.gz - containing approximately 20,000 reads

For combining tiled amplicon data:

combine_amplicons.py

This script will take profile.txt files from multiple amplicons and combine them into a single profile.txt that matches the given fasta reference file. This will work for Nextera or amplicons, and removes data from low quality positions.

Example

python combine_amplicons.py reference.fa --profiles 1_profile.txt 2_profile.txt

This command would create one new file, reference_concat_profile.txt, with combined data from each of the profiles, in this case 1 and 2.

For make histograms of mutations per molecule:

countMutsPerMol.py

This script will take mutation strings files from ShapeMapper_v1.2, and create a histogram plot of the number of mutations per molecule.

Example

python countMutsPerMol.py -n -o output.pdf example_mutation_strings.txt

This command would create one new file, output.pdf, that contains a histogram of the number of mutations per molecule.