Map reads with BWA
| 1 | map_with_bwa_mem(ref_fasta, fastq_1, fastq_2)
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| ref_fasta | reference genome or contigs | 
| fastq_1 | left reads or 1 reads of sample (pair-end reads) to map | 
| fastq_2 | right reads or 2 reads of sample (pair-end reads) to map | 
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