FAQ

Frequently Asked Questions

When to use seqkit

Seqkit is a great set of tools to manipulate fasta and fastq files. When seed sequences approach or fall below 100 basepairs seqkit is likely to result in extraction of fasta sequences compared to Magphi using BLAST.

Can I use amino acid sequences as seeds?

Yes, from Magphi v2.0.0 you can give seeds as amino acid sequences and use -p, which will make Magphi use tblastn, rather than the default blastn. So make sure you have Magphi version 2.0.0 or above if you want to use amino acid seeds

I have diverse genomes how do I handle them?

From Magphi v2.0.0 tblastn is implemented. This allows users to give seeds as amino acid sequences and the -p flag. This will increase the chance of getting a hit across diverse genomes.

Can Magphi be improved

Yes it can and if you have suggestions to how then please let us know by raising an issue here on Github or provide a solution yourself. We are more than happy to take feedback!

Where does Magphi come from

Magphi is a play on the iconic Australian bird the Magpie, which was also a nickname given to the main author when arriving in Australia. The 'phi' refers to the tool's original purpose of extracting prophages from genomes and phages often being given by the greek letter phi. 'Mag' can also relate to the main authors' first name: Magnus.