Recently published apps

We have just published the following three tools:

• SPAdes 3.15.5 – an assembly tool containing various assembly pipelines. SPAdes can be used for reads produced by different sequencing technologies, such as: Illumina, IonTorrent, PacBio, Oxford Nanopore and Sanger. SPAdes was tested on small genomes (eg. bacterial, fungal) and is not intended for larger ones.
• Unicycler 0.5.0 – a tool for bacterial genome assembly. It can assemble Illumina-sequenced reads, as well as PacBio or Nanopore long-read-only sets (for the best assemblies, it can conduct a hybrid assembly by taking both Illumina and long reads).
• Quast 5.2.0 – a tool for genome assembly evaluation. QUAST implements different methods for analyzing assemblies. By default, it utilizes Minimap2 for alignment. GeneMarkS, GeneMark-ES, Glimmer, Barrnap and BUSCO are used for gene prediction, while finding structural variations is done by BWA, Sambamba, and GRIDSS. Additionally, QUAST uses bedtools for calculating read coverage, which is presented in the Icarus contig alignment viewer.

Marko Marinkovic