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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.

splinterFasta.sh

  • Break a fasta containing multiple sequences into separate fasta files for each individual sequence. Good for splintering assemblies.

spotify_control.sh

  • Binds spotify controls to keyboard buttons in Linux.