A small C/CLI library for manipulating PAF files.

This is a C and CLI library for manipulating/reading/writing Pairwise Alignment Format (PAF). It is used by Cactus in creating the local, pairwise alignments between input sequences. It also contains some utilities for manipulating FASTA files.

Installing Paffy CLI/C Library

Do build this repo clone the repo as follows and then make:

git clone https://github.com/ComparativeGenomicsToolkit/paffy.git --recursive
cd paf && make

To test the installation, after adding the paffy/bin directory to your path, do:

make test

This will run a small number of tests.

Paffy Utilities

All Paffy utilities are run using paffy <command>, where the available commands are:

    view           Pretty print and extract stats about PAF alignments
    chain          Chain together paf alignments, useful for getting synteny info
    add_mismatches Add mismatch information to the PAF cigars (i.e. convert M to =/X format)
    trim           Slice of lower identity tail alignments
    to_bed         Build an alignment coverage map of a chosen sequence in BED format
    shatter        Break the PAFs into gapless subalignments
    invert         Switch query and target
    tile           Give alignments levels, from lowest (best) to highest (worse) by greedily picking
                   the best alignment at each location
    dedupe         Remove duplicate alignments from a file based on exact query/target coordinates
    dechunk        Manipulate coordinates to allow aggregation of PAFs computed over subsequences
    upconvert      Converts the coordinates of paf alignments to refer to extracted subsequences

In addition the FASTA utilities are run using the faffy <command>, where the available commands are:

    chunk           Break a fasta file into smaller files for parallel computation
    merge           Merge together fasta files, dealing with overlap (the inverse of chunk)
    extract         Extract subsequences from a fasta file 

For example, to pretty print a PAF alignment:

paffy view -i PAF_FILE [FASTA_FILES] -a

To understand the chunking/dechunking code for fastas and pafs see the tests/faf_paf_chunking_test.sh.

Using C Library

There is also a simple C library for working with paf files. See paf.h in the inc directory.

Cactus Local Alignment Pipeline

To understand the steps in the pairwise alignment pipeline used by Cactus see tests/paf_pipeline_test.sh. The objective is to find chains of high-quality local alignments used to anchor the multiple sequence alignment process.

Todo

Create a clean script for reproducing Cactus local alignment pipeline

Improve docs