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Achievement: Pull SharkAchievement: Starstruck

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@marschall-lab

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fawaz-dabbaghieh/README.md

Hi there! This is Fawaz. Currently a postdoc in Bioinformatics at the Steinegger Lab at Seoul National University.

I did my master's in Bioinformtaics at University of Saarland, and my PhD at Heinrich-Heine University Düsseldorf under the supervision of Tobias Marschall and Olga Kalinina. My PhD work mainly focused on developing software in the field of graph genomics and sequence to graph alignment. I developed BubbleGun for detecting bubbles and superbubbles in genome graphs (publication here). I then developed PanPA (the PanProteome Aligner) for building genome graphs from amino acid sequences and alignment of both DNA and amino acid sequences against these graphs (publication here).

I am currently part of AEGIS working on ancient genomics.

At the moment, working on gfaidx, a genome graph node-based indexer.

Languages and Tools:

c cplusplus git linux python

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  1. bubble_gun bubble_gun Public

    Python 43 3

  2. gfa_subgraphs gfa_subgraphs Public

    Extracts subgraphs or components from a graph in GFA format

    Python 24

  3. PanPA PanPA Public

    PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.

    Python 19

  4. msa_to_gfa msa_to_gfa Public

    Small python program to turn MSA to GFA v1 with paths of original sequences

    Python 2

  5. gfaidx gfaidx Public

    A new implementation of my graph indexer, I wanted to start from scratch. Now using a different Louvain Method implementation that uses much less memory.

    C++ 4

  6. graphdrawing_toolkit graphdrawing_toolkit Public

    A collection of script for drawing GFA graphs against a reference and other functionalities related to graph drawing

    Python

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