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Meet the ants

Meet the ants. Camponotus floridanus Carpenter ant. Harpegnathos saltator Jumping ant. Solenopsis invicta Red imported fire ant. Atta cephalotes Acromyrmex echinatior Leafcutter ants. Pogonomyrmex barbatus Harvester ant. Linepithema humile Argentine ant. Now meet their genomes….

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Meet the ants

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  1. Meet the ants Camponotusfloridanus Carpenter ant Harpegnathossaltator Jumping ant Solenopsisinvicta Red imported fire ant Atta cephalotesAcromyrmexechinatiorLeafcutter ants Pogonomyrmexbarbatus Harvester ant Linepithemahumile Argentine ant

  2. Now meet their genomes…

  3. Generic assembly procedure Assemble fragments into contigs Scaffolding– connecting contigs using mate-pair information

  4. Steps involved in Illumina Assembly 1) Download data (qseq file– sequences with quality scores) 2) Filter data A) Filter low quality reads B) Trim adapter sequences 3) SOAPdenovo steps A) Preassembly error correction (Identify pairs of reads sharing a common sequence (k-mer, e.g. 17-20), estimate k-mer frequency, and remove erroneous k-mers) B) Construct contigs based on short insert libraries (200-800bp) C) Join contigs into scaffolds using information from large insert mate pair libraries (1Kb-10Kb) D) Do local reassembly of unresolved gap regions using Gap Closer for SOAPdenovo

  5. 2) Filtering data (specifics) • A) Remove low quality reads • Remove reads that do not pass GA analysis Failed_Chastity filter (have an N in the last column of the GA export file) • Can use R BioConductorShortRead package (may have to convert files from qseq to fastq format) • B) Remove adapter sequences • need adapter sequence information from person that did sequencing • Can use vectorstrip in EMBOSS

  6. Computational power and time required for SOAPdenovo? Li et al 2010 Genome Research

  7. And compared to other programs Lin et al 2011 Genomics

  8. Acromyrmexechinatiorgenome raw dataNCBI: SRA Acromyrmex genome Mate pair libraries (More redundant, To build scaffolds) Shotgun libraries (Broader coverage, To build contigs)

  9. Paired end sequencing (<1Kb) Mate pair library, paired end sequencing (>1Kb)

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