Hello, I recently downloaded the pangenome graph produced by the Human Pangenome Reference Consortium (hprc-v2.0-mc-grch38.gfa.gz) and, to make my future workflows easier and faster, I …

Hi, Can anyone tell me where can I get the GO annotation terms (BP) for housekeeping genes or metabolism-related genes for bacteria? Thank you

Hi, Can anyone tell me what diffusion algorithm is used by the tool diffusion in Cytoscape? Also, I found a plugin genemania in Cytoscape, does …

Hi, Can anyone tell me how to use a GTDB as the reference database for Kraken2? A step by step guide would be very helpful. …

Hi I have been using the assembly graphs output in fastg format by (meta-)SPAdes and megaHIT. They are relatively easy to parse and manipulate in …

I'm trying to construct the variation graph as stated in "Working with a whole genome variation graph" in the github wiki of variation graph toolkit …

Briefly, I am trying to automate the process of aligning a query sequence (from FASTA) to an assembly graph (FASTG from Spades assembly). As output …

Please can anyone help me to visualize and analyze the SPAdes result?===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77 * Corrected reads are …

I'm working with the [SPAdes][1] assembler (version 3.1.1), and trying to use its FASTG graph output. Looking at the contigs.fastg file it produces, I find …

http://www.broadinstitute.org/software/allpaths-lg/blog/?p=625 The FASTG Format Specification Working Group is pleased to announce version 1.0 of the FASTG specification FASTG is a format for faithfully representing genome …