Aditya Bandla

New SILVA databases?

27

Any plans to update the rRNA databases to the current version of SILVA?

de_novo_workflow fails to parse gtdb classify output

1

Hello, I am trying to build a tree integrating my genomes with the GTDB refs. After the tree is built, the workflow fails with the error ``` ERROR: Not a...

Website down?

3

Is the dbcan2 website currently down? Currently getting a timeout error

Support for megahit

7

Are there plans to support megahit assemblies?

Database Setup

1

Hi Sorry for the rather naive question. But could you point me to any tutorials on how to setup, for example a KEGG protein family database, to use with shotmap?...

graftM create error

6

I am trying to build a graftM package for the rpsB gene from the GTDB r89 species-level genomes. I downloaded the unaligned bacterial & archaeal marker gene sequences & concatenated...

Using custom databases for annotation

4

Is there an option for users to provide their own databases for the annotation step. I would like to use more recent versions of PFAM and dbCAN for my dataset

Error in rank(x, ties.method = "min", na.last = "keep") : unimplemented type 'list' in 'greater'

6

Installed treeshrink using conda called it using `run_treeshrink.py -t min_marker_80_sub_hundred_RAxML_bestTree.sp_faa_refined.tre` but got this error ``` Launching TREESHRINK version 1.3.1 There are only 1 gene trees in the dataset. TreeShrink will...

Hi Stephen, Thanks for the great tool. I have a set of species-level MAGs that range in completeness from 50-100% and redundancy/contamination 0-10%. These are species representatives chosen using dRep...

Wrong scaffold coverage calculation when using coverage file

5

I ran the refinem scaffold_stats & outliers command with a custom coverage file using the --coverage_file option. Some contigs got flagged as having zero coverage across all samples. However, when...