I performed de novo genome assembly on a bacteria sample (two files: reads.1.fq and reads.2.fq), got resulting the "contigs.fasta" file, used BWA to map the two initial fq read files to "contigs.fasta". Now I have the resulting SAM file from BWA.
How can I perform alignment between those two files and compare my "contigs.fasta" file with the SAM file resulting from BWA?
How can I perform alignment between those two files and compare my "contigs.fasta" file with the SAM file resulting from BWA?
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