map_with_bowtie2: Map reads with Bowtie2
In abshah/RADseqR:

Map reads with Bowtie2

1 2	map_with_bowtie2(ref_fasta, idx_name, fastq_1, fastq_2, Threads, sam_outfile, rg_id, rg_lb, rg_sm, rg_pl)

`ref_fasta`	reference genome or contigs in fasta format
`idx_name`	index name for alignment
`fastq_1`	left or 1 reads
`fastq_2`	left or 2 reads (for pair-end reads only)
`Threads`	number of concurrent threads to run with (depends on server resources)
`sam_outfile`	resulting filename (in SAM format)
`rg_id`	sample id name
`rg_lb`	sample library name
`rg_sm`	sample pool name
`rg_pl`	Platform/technology used to produce reads. Valid values: "CAPILLARY", "LS454", "ILLUMINA", "SOILD","HELICOS","IONTORRENT","ONT","PACBIO"