CAMISIM

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The NCBI taxonomy is deeply ingrained into CAMISIM. It would be nice to have some support for the GTDB taxonomy as well

AlphaSquad

Cover viral genomes

10

Hello, I am planning to create my microbial-genomes population composed by viruses, bacteria and ribosomes to test our metagenomic pipeline. To achieve this objective, we are going to use a...

emiliomastriani

Gold standard assembly and binning ran despite being set to false

1

Hi CAMISIM, Thanks for the great tool. I have just started to use it to generate metagenomes based on a custom profile. Since I am using genomes of assemblies of...

elximo

Include the latest PBsim version with new error model(s): https://doi.org/10.1093/bioinformatics/btaa835

AlphaSquad

[MetagenomeSimulationPipeline] [Errno 24] Too many open files in line 99

10

Hi, First of all thanks for developing and maintaining this tool! I'm simulating a 5 samples (5Gbp each) using two communities derived from the supplied genomes, but eventually, after the...

mgabriell1

[documentation] Give correct arguments to read simulators

3

I'm trying to use CAMISIM to generate a big fastq file containing community reads with no error. If I understand well, this is possible using wgsim read simulator with the...

yoann-dufresne

Include a pre-built database for ete3.

1

And finally, it would be great to include a pre-built database for ete3. Currently, it is generated during the first execution. Thanks again, Florian _Originally posted by @fplaza in https://github.com/CAMI-challenge/CAMISIM/issues/125#issuecomment-990901418_

AlphaSquad

File of Files for CAMISIM

2

To improve documentation, simplify usage and increase understanding of code, we should create a file of files for all scripts, defaults and tools provided within CAMISIM

AlphaSquad

Using CAMI format input for metagenome_from_profile.py

3

Hi, I was trying to run metagenome_from_profile.py using a .profile input file as the manual says it accepts either biom format or CAMI format. However, I received this error message...

raquellewei

Fasta name-entry formatting

2

Hi and thank you for a super useful tool! I have had issues with making the de-novo profiling work on a list of genomes with a strange error during the...

joacjo