BAM, BWA and SAMTOOLS: my notebook

Here are my notes about MAQ,BWA and SAMTOOLS. MAQ Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. Here I used chrM.fa, the reference sequence for the mitochondrial genome >chrM GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCAT