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 ?