useful_scripts

• this repository will host simple scripts and workflows for simple repetitive tasks

Contents

Snakes

querying_assemblies

• A snakemake workflow to find a query sequence within an assembly or fasta file. Returns the name of the sequenes containing the query, alongside coordinates and hit scores.

plot_pairs

• Finds potential homoeologous scaffolds in an assembly.

cov_vs_length

• Generates coverage information from an assembly and read library and then plots the coverage depth against the length of the scaffolds.

Scripts

splinterFasta.sh

• Break a multifasta file into multiple individual files for each sequence it contains.

blastProgressCheck.txt

• A script to check the progress of a blast search.

countLengths.py

• A python script to find the lengths of all sequences in a fasta.

countSeqs.py

• Count the sequences in a fasta file using python.

extractSeq.py

• Extract a named sequence from a fasta file into an individual file.

fixSwap.sh

• Clears out linuz swap memory when Linux is being weird.

mouse_fix.sh

• Slows the mouse sensitivity down lower than the stock settings allows you to. Elbow turner approved.

mappingCounts.py

• Maps short read samples to reference genomes and generates counts of input reads and mapped reads.

spotify_control.sh

• Binds spotify controls to keyboard buttons in Linux.