metaGEM

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MAG abundance across samples

1

Hi! It seems the 'abundance' rule maps each sample's reads against the bins generated from that same sample. Reads are not mapped against bins generated from other samples. Is this...

zoey-rw

Update needed to modelVis rule for models reconstructed using CarveMe version>=1.5.0

1

Hello, again Francisco! I think I figured out the problem with the _modelVis_ rule. Just small corrections are needed for users working with a carveme >1.5.0. Changes (In the _Snakefile_):...

shreyanshumale

#159

franciscozorrilla

[Bug]: Metawrap Installation failure

3

Hello! I am trying to install metaGEM using the instructions provided in https://github.com/franciscozorrilla/metaGEM/blob/master/config/README.md I have managed to get everything installed up until section 3, metawrap. When running `conda create -n...

Amit-H

feature: test and compare new binners

4

The binning landscape has changed since the initial development of metaGEM. It would be a good idea to get a shortlist of novel binning tools for testing, with the ultimate...

franciscozorrilla

feature: test & enable bioconda installation on macbook

1

Would be great if users could conda install metagem locally on apple ARM architecture machines, initially suggested here #122 This is not meant for standard usage, but could be helpful...

franciscozorrilla

# 🩻 Single batch submission of GTDBTk-based taxonomic classification 🚀 Current GTDBTk rule is great when dealing with many metagenomes, but when dealing with many isolate samples it makes more...

franciscozorrilla

# 🥚 eggNOG-mapper for better functional annotation 🍸 ## 🐍 Snakefile tasks - [x] create eggnog-mapper rule for processing ORF-annotated protein fasta files of genomes - [ ] create helper/supplementary...

franciscozorrilla

# 🦠 Isolate genomes subworkflow 🔦 Adding support for isolate genome assembly in the next version of metaGEM 💎 ## 🐍 Snakefile tasks - [x] create shovill rule for dealing...

franciscozorrilla

improvement: use `wc` to count bp instead of summing contig header info for abundance

1

For abundance calculation we need to get bp of genome, currently we do this based on the contig headers info, although this can become problematic for genomes assembled by different...

franciscozorrilla