Ex Center for Algorithmic Biotechnology
@bioinf_spbu
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Former members of Center for Algorithmic Biotechnology
Joined July 2012
RT @spadesassembler: SPAdes 4.0 is released! Since 2022 SPAdes is not related to any institution and is maintained…
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New IsoQuant 3.4 is released! It features improved computational performance and quantification algorithms:
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RT @hagentilgner: Andrey & Alla put out the newest version of Isoquant (; Results unchanged but memory usage down ~…
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IsoQuant paper is out in @NatureBiotech! IsoQuant is a tool for accurate annoation-based and de novo transcript disovery from long RNA-Seq reads and is available at
Out in @NatureBiotech: What isoforms are really in your @PacBio or @nanopore run? Andrey&Alla (with help by @noush_joglekar, AS, @jjarroux &AL) have precise answers: #LongRead #RNA @iRnaCosi #nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing
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BandageNG v2022.08 is out! This release was mainly focused on improving graph search subsystem: * Significantly reworked BLAST search * Added minimap2-based sequence alignment * Added HMMer sequence search (both nucleotide and protein) Get it at
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Bandage-NG 2022.07 is out. Lots of new features including new path query UI, support for loading GAF and SPAligner TSV paths and many other things including usual improvements in memory consumption and processing speed.
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What happens if outdated tools are used in analysis? One have to invent some sophisticated pipelines to deal with suboptimal results. Here we show that simple use of latest version of rnaviralSPAdes / coronaSPAdes produces perfect viral assemblies without any additional steps.
Benchmarking state-of-the-art approaches for norovirus genome assembly in metagenome sample #bioRxiv
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RT @biorxivpreprint: Benchmarking state-of-the-art approaches for norovirus genome assembly in metagenome sample #…
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Bandage-NG switched to time-based versions. With version 2022.06 we're having: - Support for GFA v1.2 features - Faster multithreaded layout - Possibility to save / load graph layout - Usual improvements of memory consumption & speed
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- Changed arrowheads - Some bugfixes and UI improvements PS: Our next aim is to speed-up / improve graph layout process 2/2
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@erikgarrison @tobiasmarschal @rrwick @wafemand @spbifmo_en btw, is there any interest in adding some rGFA support? E.g. tag-based coloring, etc.? If yes – please open issue and explain your ideas, please :)
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@tobiasmarschal @rrwick @wafemand @spbifmo_en Patches are always welcome :) We have now more-or-less universal "annotation" subsystem. So one need to make use of it. Right now it is possible if GAF is converted to BED regions.
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@IvanSovic @rrwick @wafemand @spbifmo_en Please file the issues (. Though these two ones are already planned ;)
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Note that the changes were quite invasive and some fallout is expected. Please do file the issues! ;)
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@GenomeRIK @noush_joglekar @nanopore Nope, sorry, used the one from the paper. Forwarded to the one from GitHub now!
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