Journal: Bioinformatics Advances

Article Title: Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data

doi: 10.1093/bioadv/vbaf004

Figure Lengend Snippet: Sphae workflow overview. The workflow processes sequencing reads from short- and/or long-read data in fastq format. The command sphae run, starts with quality control, filtering out low-quality reads and adaptor sequences. Processed reads are assembled, and the resulting assemblies are processed to confirm complete phage genomes in each sample. The phage genomes are annotated to identify the genes and assign biological functions. The final output folder contains the assembled genome (fasta format), annotations (GenBank format), a Circos plot (PNG format), and a summary text file detailing phage characteristics.

Article Snippet: Oxford Nanopore raw sequencing output is in fast5 or pod5 format, which must be basecalled using Guppy or Dorado to convert the reads to fastq format before running this workflow.

Techniques: Sequencing, Control