SeqTools {🧬:🛠️}

A small collection of tools for working with sequence files in a Python-based environment.

Tools:

• seq_gen: Generate DNA sequences - either pure sequences, or fasta/fastq formats
• seq_sub: Subsample reads files
• tools (misc.)
  • k-mers: tools for generating k-mers from a string, as well as counting non-unique k-mers
  • Visualisation: plot histograms for read length and PHRED-score

Requirements

• The Big 3 (+1)
  • pandas
  • numpy
  • matplotlib
  • seaborn
• Biopython - tools for loading, manipulating and exporting read data
• tqdm - used for pretty progress bars (currently only in rare cases)

For convenience, a conda environment file has been included.

$ conda env create -f environment.yml