Open Xcode, select “Xcode -> Preferences -> Downloads -> Command Line Tools -> Install”.ĭisable line wrap to make it easier to select the full sequence. snpEff 4.2: determine the effect of SNVs.samtools 1.3.1: manipulate SAM/BAM alignment files.Java 7 or later: execute Java programs.BWA 0.7.15: align short reads and long contigs.bcftools 1.3.1: manipulate VCF/BCF variant call files.ABySS 1.9.0: genome sequence assembler for short reads.4 GB of RAM and 5 GB of disk space is required. The total run time of the tools alone is approximately 70 minutes on a 2-core 2 GHz system. Exercise 13: Align the reads to the contigs using BWA (optional). Exercise 12: Compare the assembly variants to the read-alignment variants (optional).Exercise 11: Determine the effects of the SNVs.Exercise 10: Call variants of the contigs-to-reference alignments using bcftoolss.Exercise 9: Call variants of the reads-to-reference alignments using bcftools (optional).Exercise 8: View the contig to reference alignments SAM file.Exercise 7: Browse the contig to reference alignments using IGV.Exercise 6: Browse the contig to reference alignments using samtools tview.Exercise 5: Align the contigs to the reference using BWA-MEM.Exercise 4: Align the contigs to the reference using web BLAT.Exercise 3: Assemble the reads into contigs using ABySS.Exercise 1: Align the reads to the reference using BWA (optional).Exercise 0: Index the reference using BWA.snpEff is used to determine the effects of these variants.Īfter this lab, you will have learned how to use ABySS to assemble a small genome, use BWA-MEM to align reads and contigs to a reference genome, use IGV to visualize these alignments, and use bcftools and snpEff to call variants and determine their effect. IGV is used to visualize these alignments and variants. BWA-MEM is used to align the assembled contigs to the human reference genome, and bcftools is used to call variants. We will use ABySS to assemble a 200 kbp bacterial artificial chromosome (BAC) using one lane of paired-end reads from the Illumina platform. This workshop is designed by Shaun Jackman Purpose ABySS De novo assembly of Illumina reads using ABySS and alignment using BWA
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