Analysing multiple metagenomes individually made into contigs

[AlexandreThibodeauUdM]

HEllo!

Thanks you for this wonderfull tool!

I am starting to analyze a set of 47 samples, shotgun Illumina paired sequencing on my computer before moving to a cluster (if I need to)

I trimmed the reads with trimmomatic, removed my host with bowtie2 and assembled my contigs using SPADES.

Now I wish to use squeezeMeta but using all my assembled genomes. Is there a way to do so? I know there is an option to include a path to 1 contig file, but how about my other 46 assembled other files?

If I run 47 times Squeezemeta, is there a way to put all results into the same project afterwards?

Cheers!

[jtamames]

Hello Yes, look in the manual, page 10. You can set a different external assembly file for each of your samples. Best, J

[AlexandreThibodeauUdM]

ok thanks I will look into it

[fpusan]

Closing due to lack of activity, feel free to reopen