-
Hi,
I'm assembling metagenomes from ancieant microbiome samples. I have successfully assembled genomes from almost all of my samples, but am struggling with two of them. One of the failures is givi…
-
Hi,
I used VirSorter v2.1 on contigs from environmental metagenomes. I selected potential viral contigs with score >0.8. I then verify completeness with checkV. Several potential viral contigs whe…
-
When I run:
metawrap /home-2/eerteki2@jhu.edu/scratch/metaWRAP/pipelines/binning -a AS.contigs.fasta -o AS_binning --metabat2 /home-2/eerteki2@jhu.edu/data/BAC_Metagenomes/CLEAN_READS/AS_1.fastq /h…
-
I'm trying to use parsnp to infer core genes (and importantly, get rid of signal introduced by recombination in core genes) on around 1000 bins retrieved from metagenomes. The problem is that parsnp t…
-
I am trying to run an assembly with only larger kmers, but the MEGAHIT appears to use the default kmer list. Is there something that I am missing? Code and options.json shown below. Thanks!
Code:
…
-
Hi,
I was wondering if MeshClust could be used to cluster MAGs in order to dereplicate them? There is no mention of metagenome assembly in your paper and I'm wondering if the distance estimation wou…
-
hey @AlessioMilanese
I wanted to confirm if the minimum length used by all 10 marker-genes in mOTU2 is the same as [mOTU1 paper](https://www.nature.com/articles/nmeth.2693)?
Based on the [supplem…
-
Hello!
Thanks for developing this method. I found it extremely useful for my work.
I was wondering if you have tested this method using open-source solvers like [GLPK](https://www.gnu.org/softwa…
Vini2 updated
8 months ago
-
``` r
library(tidyverse)
setwd("C:/Users/Julia/Dropbox/A-PhD_WIPs")
SI
-
Hey,
I'm trying protein clustering for the first time and need some advice. I would like to cluster bacterial proteins from 20 different metagenomes to obtain representative clusters across all samp…