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BWA can be used to align both single-end and paired end reads to a reference genome or Paired end alignment; Running BWA batch jobs in Puhti. Manual bwa index -a bwtsw database.fasta. bwa aln database.fasta short_read.fastq > aln_sa.sai. bwa samse database.fasta aln_sa.sai short_read.fastq > aln.sam.BWA is a reference genome assisted assembler for read data. It maps reads to a given reference genomes. Standard Settings (in pipeline and manual mode). BWA can map low-divergent sequences against a large reference genome, such as the human genome. 0 It consists of three algorithms: 1. BWA-backtrack (Illumina Exploring the variant calling workflow; Choosing appropriate BWA alignment Details on BWA and its functionality can be found in the user manual; The first step of using BWA is to make an index of the reference genome in fasta format. Additional options for bwa mem can be found in the BWA manual. BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for

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