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" |
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