Assembly at lineage level from shotgun data ?

Question

[v.berriosfarias]

Hello I have metagenomic reads under some fastq files, from these fastq files I want to map all reads that match against the genome of a fungal species so I retrieve only the mapped reads that matched against this reference genome using bowtie2.

As the resulting fastq files only have reads that match against the fungus species genome, I want (if possible) to assembly these reads so I can assembly MAGs that represent the lineages of this species.

Is there a way or tool to assembly genomes at lineage level from the resulting fastq files ?

Answer 1

[Mensur Dlakic]

The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a reference genome and some reads, it will recruit the reads that map to the reference, assemble it, and then repeat the process several times. It should work even for eukaryotes, except there there is no chance you will get a closed circular genome which is a specified goal for this tool.

https://pubmed.ncbi.nlm.nih.gov/33961626

There are non-automated ways of doing this, but that takes more time to explain and many independent resources.