Sanger Check: Package for Automating Analysis of Sanger Sequencing Data

Examples:

See examples/sanger_check_demo.ipynb for introduction to using sanger_check.

Colab Notebook

Availible Functions

sc.parse_fasta(fasta_file)

• Parses a Fasta file and returns a pandas DataFrame
• Can be used with Azenta multifasta file
• 

sc.auto_assign(sanger_df, seq_df)

• Parsed multifasta for sanger sequences and dna sequences can be automatically matched together using pairwise alignment
• Returns a dataframe that maps sanger sequence names to reference dna and DNA orientation (forward/reverse)

sc.check_sanger_sequence(dna_seq_name, dna_seq sanger_seq_name, sanger_seq, plot=False)

• Prints information and plots alignment between reference sequence and sanger sequence