https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping? https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping Sun, 28 Apr 2019 12:37:57 -0500 https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam]]> Rahul Nayak