-U is the argument before your unpaired files (if you still want to use them).-2 is the argument before your reverse input file (usually trimmed paired R2).-1 is the argument before your forward input file (usually trimmed paired R1).-x is the argument used to specify the path to your reference index previously built by Bowtie (see above).G3: Genes, Genomes, Genetics early access. It allows to keep as unaligned reads that may be chimeric between virus and host (depending on your library preparation, these can exist see: Peccoud J, Lequime S, Moltini-conclois I, Giraud I, Lambrechts L and Gilbert C (2018) A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation.
–end-to-end is a full read alignment: the read must match in its entirety to the reference. –end-to-end specifies the alignment type.In case you work on one thread, you can drop off the argument. The integer following it is the number of threads to use for this command. -p is to use if you want to multithread your command (it will speed up the process).Let’s have a look on all the arguments of this command: unpaired_filtered.fastq > host_aligned.sam Bowtie2 -p 40 -end -to -end -x /pathToRef /host -index - 1 R1_paired.fq - 2 R2_paired.fq -U unpaired.fq -un -conc.