How-to…

…Run software natively

If you need to run software in a way Metabiome does not support, you can run it natively by simply activating the environment where it lives and then using it normally. In the following example taken from the Bowtie 2 manual, we need to use this software to create an index for the Lambda phage reference genome, and not for decontamination of reads as implemented in Metabiome:

# Activate environment
conda activate metabiome-preprocessing
# Run Bowtie 2 natively
bowtie2-build $BT2_HOME/example/reference/lambda_virus.fa lambda_virus

You can find a complete list of Metabiome modules and software in Metabiome modules.

…Perform co-assembly of samples

If you need to perform an assembly using the reads from all or many samples at once, then you can concatenate the files together and run the assemblers as if it where just one paired-end sample. For example, assuming you have files named according to the _1./_2. naming convention:

# Create directory to store new files
mkdir co-assembly

# Concatenate all _1. files
cat *_1.fq.gz > co-assembly/all_1.fq.gz

# Concatenate all _2. files
cat *_2.fq.gz > co-assembly/all_2.fq.gz

# Run assembly
metabiome metaspades -i co-assembly -o assembly_results

…Create read-based coverage files for genome binning

If you want to create read-based coverage files to boost the binning of your contigs, you can do it easily through our pipeline Metabiome. Metabiome has three different software (CONCOCT, MaxBin2 and MetaBAT2) for genome binning. So, let’s just take a look on how to create these read-based coverage files and bin our contigs alongside:

For CONCOCT and MaxBin2 is pretty straightforward because the commands concoct and maxbin2 create the read-based coverage files automatically like so:

# Run CONCOCT
metabiome concoct -i contigs_reads/ -o concoct_out/

# Run MaxBin2
metabiome maxbin2 -i contigs_reads/ -o maxbin2_out/

Whereas for MetaBAT2, if you want to perform the binning with read-based coverage files, you must generate them previously. To do so you can use our command coverm like so:

# Run CoverM
metabiome coverm  -i contigs_reads/ -o read_coverage/

Now, let’s use this read coverage files to run metabat2 command. But keep in mind that MetaBAT2 requires the contigs in gzip format in order to run:

# Run MetaBAT2
metabiome metabat2 -i gzip_contigs/ -co read_coverage/ -o metabat2_out/

Moreover, if you already have your read-based coverage files, you can also provide it to any of the binners and automatically skip the process of creating these read-based coverage files.

…create scaffolds-to-bin tsv files for DAS Tool

Besides of contigs in fasta format, DAS Tool requires a tab separated scaffolds-to-bin file from each metagenomic binner. To create these files, you must have the bins from each metagenomic binner in distinct directories. Now, we will use the bins from MaxBin2’s output (maxbin_bins/).

# Move to directory containing bins
cd ~/maxbin_bins/

# Activate environment
conda activate metabiome-das_tool

# Create scaffolds-to-bin tsv files
Fasta_to_Scaffolds2Bin.sh -e fasta > ERR981212_scaffolds2bin_maxbin2.tsv

# Deactivate environment
conda deactivate metabiome-das_tool

In this case, we have succesfully created scaffolds-to-bin tsv files of MaxBin2’s ouput from sample ERR981212. You can now do it with other metagenomic binners. Keep in mind that, for example, MetaBAT2 generate bins with fa extension. So, you must change the -e flag from fasta to fa.