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Mapping-Assisted Targeted-Assembly for Metagenomics
Dear All, I am trying to reconstruct 16S rRNA gene sequences from metagenome and then use those predicted 16S to find functional profiling using picrust2. So I followed the following...
Hi, I want to get the default SSU rRNA reference database, so I run the following code: `index_default_ssu_rrna_db.py -d /mnt/d/11tool/Anaconda_linux/anaconda3/envs/markerMAG/opt/matam-1.6.0/db --max_memory 10000` I then get the following error: 
Hi, I'm trying to figure out which one of the output files includes the assembled 16s rRNA sequences obtained with the pipeline, as I would like to use these sequences...
Dear author, I want to ask what is the default fastq file, only foward reads or reverse reads or interleaved reads? Thanks, Jianshu
Our Bioconda recipe does not use the same process to build MATAM. For maintenance purpose it will be better to use the same process.
Right now, we are using SortMeRNA to align contigs against the complete ref db, and we are outputting all alignments. This can lead to very big SAM files because some...
**Is your feature request related to a problem? Please describe.** When the input FASTQ file does not exist, MATAM does not stop properly its execution **Describe the solution you'd like**...
ppericard/sortmerna was forked from biocore/sortmerna and modified to change the OpenMP parallel schedule in order to greatly improve sortmerna time during MATAM scaffolding. However, in the conda recipe, MATAM uses...
The alignment filtering step should sort the SAM file by read id and alignment score before filtering. Right now the sorting is performed by the following command: `2019-07-29 13:47:23,161 -...
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Mapping-Assisted Targeted-Assembly for Metagenomics