actledge

How can I color the branches of the tree directly as in the example？

2

Just like the first example in the example page in phandango：Gubbins + BRAT NextGen I try to use the example file ，but the branches of tree were not colored. I...

version 3.15.5 --metaviral still produce duplicated scaffolds with different cutoff.

2

### Description of bug there are the title line of scaffolds.fasta produce by SPAdes 3.15.5 with --metaviral. The last two sequences were duplicated. >NODE_1_length_52915_cov_2931.632379_cutoff_0_type_circular >NODE_2_length_4936_cov_363.953421_cutoff_0_type_circular >NODE_1_length_148899_cov_7.069247_cutoff_5_type_linears >NODE_1_length_52991_cov_2927.538344_cutoff_54_type_linearrepeat >NODE_1_length_52991_cov_2927.538344_cutoff_70_type_linearrepeat By the...

How should genomad be used appropriately, when there are a huge number of assemblies to be processed.

1

Hi, I have similar questions with Issue26(https://github.com/apcamargo/genomad/issues/26#issue-1796936020). But I have a large number of assemblies to explore for prophages using genomad (It could be several hundred GB or even a...

Is it reasonable to use LINCLUST with --Kmer-Per-Seq 2000?

4

Since cluster module needs too much memory. (I have 2 million nucleotide seqs, about 30G, and 1T memory, and segment fault occurred). I try to use LINCLUST instead. But I...

MMseqs cluster : Invalid database read ... Error: Offset step died

11

My command: ``` mmseqs createdb 1831648_seqs.fasta 1831648_seqs.mmseqs2db mmseqs cluster 1831648_seqs.mmseqs2db 1831648_seqs.mmseqs2clu tmp --cov-mode 0 -c 0.85 --min-seq-id 0.95 --threads 112 ``` My fasta file have 1.8 million sequences, and the...