Assembly: before and after
- 1. Assembly – before and after Lex Nederbragt lex.nederbragt@ibv.uio.no @lexnederbragt
- 2. A warning The list is by no means complete Nor do we have experience with all the programs mentioned
- 3. Sample DNA Reads Genome assembly Sequencing AssemblyDNA isolation QC QCQC
- 5. Fastqc
- 6. Prinseq
- 11. Adapter/quality trimming http://www.biostars.org/p/53528/ Celera assembler Overlap based trimming Fastx Toolkit Seqtk PrinSeq NGS QC Toolkit Trimmomatic BioPieces Cutadapt … …
- 12. Mate pair splitting and orientation 150 – 600 bases Illumina paired end reads 2 – 40 kilobases Illumina mate pair reads 2 – 40 kilobases 454 mate pair reads linker
- 13. Mate pair splitting and orientation Illumina paired end reads Illumina mate pair reads 454 mate pair reads linker junctionjunction + + paired end reads ‘contamination’
- 14. Mate pair splitting and orientation Illumina paired end reads Illumina mate pair reads 454 mate pair reads linker junctionjunction + + paired end reads ‘contamination’ Check what orientation your assembler expects for the reads!
- 16. Error-correction Stand-alone or built into assembler
- 17. Merging pairs List from Torsten Seeman’s blog http://thegenomefactory.blogspot.no/2012/11/tools-to-merge-overlapping-paired-end.html COPE http://sourceforge.net/projects/coperead/ SeqPrep https://github.com/jstjohn/SeqPrep FLASH http://www.cbcb.umd.edu/software/flash fastq-join http://code.google.com/p/ea-utils/wiki/FastqJoin PANDAseq https://github.com/neufeld/pandaseq mergePairs.py http://code.google.com/p/standardized-velvet-assembly-report/source/browse/trunk/mergePairs.py Recent addition
- 20. Estimate kmer to use preqc (SGA) http://arxiv.org/abs/1307.8026
- 21. Reads Genome assembly Assembly What can the reads tell us about the genome
- 25. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 26. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 28. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 30. Correcting bases Quiver from Pacific Biosciences
- 32. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 34. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 37. Gene finding
- 38. Binning Bacteroides Proteobacteria Cyanobacteria Per-con g read depth Nederbragt et al, 2010
- 39. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 41. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 42. Comparative measures Log Average Probability (LAP) Assembly Likelihood Evaluation (ALE) See also Howison, Zapata2 and Dunn (2013) Toward a statistically explicit understanding of de novo sequence assembly doi: 10.1093/bioinformatics/btt525
- 43. Genome assembly Comparing to each other Metrics Merging Improvement Visualization Validation Comparing to reference
- 44. Reference comparison Mauve assembly metrics
- 45. Review
- 47. Too many tools… http://wwwdev.ebi.ac.uk/fg/hts_mappers 88 short-read mappers
- 48. Embargo!