pafgnostic
supports both uncompressed and gzipped PAF (Pairwise mApping Format) files, and it outputs a comprehensive set of metrics for each alignment, including the number of matches, mismatches, insertions, deletions, unique events, and various lengths and averages for these events.
pafgnostic
is written in Rust, so you can install it using cargo
:
git clone https://github.com/AndreaGuarracino/pafgnostic
cd pafgnostic
cargo install --force --path .
Run pafgnostic
with a PAF file (compressed or uncompressed) as input:
pafgnostic --paf input.paf
pafgnostic
outputs a tab-separated table directly to the console with the following columns:
- Query name, start, end, strand
- Target name, start, end
- Number of matches, mismatches, insertions, deletions
- Unique matches, mismatches, insertions, deletions
- Longest, shortest, and average lengths of matches, mismatches, insertions, deletions