First note in HackMD. Let see if this space is useful or just yet another forgetable thing that will accumulate digital dust.
This note is designed to set up a Google environement to perform metagenomic co Assembly on mouse stool sample. Each individual mouse was sample multiple point in time allowing to boos the microbial signal.
The data
folder need to exist first
Should move to mamba
It's a genome assembler design to reconstruct small genomes. Good for curated target assembly.
Paper
Github
Another assembler, less strict and faster than spades. Good for initial rough assembly
Paper
Github
BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. I layman terms it is a fast mapper, we have to download manually for sourceforge. Available here.
Home page
Quast evaluates genome/metagenome assemblies by computing various metrics.
Binny is a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes
Paper
Github page
Binny needs a yaml file to run its snakenake based pipeline. So I have edited one adjusted to the IND01 samples in a file called config_ind01.yaml
. This file will then be the base for creating a yaml file for all subsequend individuals.
Download mouse Genome to remove unnecessary read from the library.
I follow the following folder system for my pipeline:
Preparation of the folder setup
In this step we remove the host reads, which help the assembler assembling microbial genomes. Here we ask bbmap to map our R1 and R2 raw read file to the mouse reference genome and output a single interleaved filtered read fastq.gz
file.
The one loop that:
tutorials
Metagenomic
Assembly
Mapping
Mini
pipeline