Krešimir Križanović

Great thread! Nice summary of the work.

After many months, I'm proud to share our work on untangling genome assembly graphs with GNNs. Or, GNNome Assembly (sorry not sorry)🧬 Paper: arxiv.org/abs/2206.00668 Code/Data: github.com/lvrcek/GNNome-… with @xbresson, T. Laurent, @Martin_fschmitz, and @msikic. Read more in 🧵

I am hiring a postdoc at the GIS Singapore. Join us in developing a new generation of haplotype resolved de novo assemblers using a combination of classical algorithms and AI. More about this and other open positions on sikic-lab.github.io/Postdoctoral/ DM or email me.

Looking for a metagenomics classifier for long reads? Minimap2 or even Ram are worth trying too... biorxiv.org/content/10.110… w/ @NiranjanTW @KrizanovicK @jmaricb @Sylvain14518009

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De novo assembler Raven is published at NatCompSci rdcu.be/ckZT1. Easy to use, fast and memory efficient. Try it with metagenomic data too. w/@robertvaser !!!

Dedicate enough time to database preparation biorxiv.org/content/10.110… w/ @jmaricb @KrizanovicK @Sylvain14518009 @NiranjanTW

Raven - rapid and easy to use long read de novo assembler which produces the least number of contigs biorxiv.org/content/10.110… w/ @robertvaser. Any comments are more than welcome!

Do not miss opportunity to learn about de novo assembly with @robertvaser (Racon, Ra, Raven) and @jmaricb (Graphmap2) !

Raven - long read de novo assembler. github.com/lbcb-sci/raven - with @robertvaser. Raven is an upgraded version of Ra which is now one binary without any intermediate files plus some additional improvements. Any feedback is more than welcome!

Graphmap2 - first version of new splice-aware RNA mapper with fine-tuned detection of exons and their boundaries biorxiv.org/content/10.110… github.com/lbcb-sci/graph… w/ @IvanSovic @jmaricb and @NiranjanTW

Let us present the first release of our long read scaffolder github.com/lbcb-sci/ScaRa All feedback is welcome !! w / @KrizanovicK and @ikrpelnik1 . @nanopore @pacbio

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Racon 1.0 released – faster, consumes less memory, added support for FASTA format and Illumina reads for both error correction and consensus/polishing. Read about it here: complex.zesoi.fer.hr/index.php/en/b… with @robertvaser, @IvanSovic and @NiranjanTW

Long-read RNA-seq splice aware mapping - very close competition between GMAP and Minimap2! complex.zesoi.fer.hr/index.php/en/b… in addition to academic.oup.com/bioinformatics… with @KrizanovicK @aechchiki @_julien_roux

our long-read RNA-seq mappers evaluation academic.oup.com/bioinformatics… new RNA-seq mapper soon ;) with @KrizanovicK @aechchiki @_julien_roux

Edlib: Lightweight super fast library for exact global and semi-global sequence alignment published at academic.oup.com/bioinformatics…: @MartinSosic

GraphMap v0.4.0 can now accept GTF files and map RNA-seq data to transcriptomes! @msikic @NiranjanTW @me_myself_andY github.com/isovic/graphmap

Nice work! twitter.com/msikic/status/…

A map of 20 selected assembly papers from 1979-2013. Theory / Algorithm / Assembler / Genome.