12/9/2023 0 Comments Samtools macos homebrewExercise 5: Align the contigs to the reference using BWA-MEM This assembled contig contains both the BAC cloning vector and the human DNA insert. What is the cause of this chimeric contig? What is the best alignment of our non-human contig fragment? Look at the first few best hits, and ignore hits to chimpanzee ( Pan troglodytes) clones. Select the database “Nucleotide collection (nr/nt)”. Aligned sequence is shown in blue upper-case characters, and unaligned sequence is shown in black lower-case characters. Select that contig, and copy the unaligned sequence to the clipboard. Which contig has unaligned sequence at one end? The one-pixel-wide purple line is absurdly difficult to see. Unaligned query sequence is shown with a ridiculously thin purple line at the end of the alignment. Zoom out to see the alignment of both contigs. Zoom in to see the sequence of the feature. What feature overlaps the gap that likely caused the assembly gap? Set the “RepeatMasker” track in Repeats to “full”. Zoom in on the gap between the two contigs. Set the “Common SNPs” track in Variation to “pack”.Ī SNV between the assembled sequence and reference sequence is displayed with a red line. To which chromosome and band do these contigs align? What is the exact length of these two contigs?Ĭlick “browser” for the best alignment and then zoom out 10x. Select the two contigs whose lengths are approximately 8 and 16.5 kbp and copy-and-paste their sequence into BLAT. For Emacs, select the option “Options -> Line Wrapping in this Buffer -> Truncate Long Lines.” For Vim, select the option “Edit -> File Settings -> Toggle Line Wrap”, or type :set nowrap 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
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |