floridanus Carpenter ant Harpegnathos saltator Jumping ant Solenopsis invicta Red imported fire ant Pogonomyrmex barbatus Harvester ant Linepithema humile Argentine ant Atta ID: 798811
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Slide1
Meet the ants
Camponotus
floridanusCarpenter ant
Harpegnathos
saltatorJumping ant
Solenopsis
invictaRed imported fire ant
Pogonomyrmex
barbatusHarvester ant
Linepithema
humileArgentine ant
Atta
cephalotes
Acromyrmex
echinatior
Leafcutter ants
Slide2Now meet their genomes…
Slide3Species
Citation
Platform(Coverage)Assembly Program(s)
Scaffold Length N50 (total)Harpegnathos
saltatorJumping antBonasio et al 2010 Science
Illumina(104x)
SOAP de novo6 lib.- 3 paired end, 3 mate pair598 Kb(297 Mb)Camponotus
floridanusCarpenter ant
Bonasio et al 2010 Science
Illumina
(102x)
SOAP de novo- 3 paired end, 3 mate pair
603 Kb(238 Mb)
Acromyrmex
echinatiorLeafcutter antNygaard et al 2011 Genome ResearchIllumina(123x)SOAP de novo5 lib.– 2 paired end, 3 mate pair1.1 Mb(300Mb)Atta cephalotesLeafcutter antSuen et al. 2011 PNAS454(18-20x)Roche GSAssembler5.1 Mb(317 Mb)Solenopsis invictaFire antWurm et al. 2011 PNAS454 + Illumina(~55x)SOAP denovo + Roche GS Assembler720 Kb(353 Mb)Linepithema humileArgentine antSmith et al. 2011 PNAS454 + Illumina(23x)Roche GS Assembler + Celera CABOG1.3 Mb(43 Mb)Pogonomyrmex barbatusHarvester antSmith et al. 2011 PNAS454(10-12x)Celera CABOG 793 Kb(235 Mb)
Slide4Generic assembly procedure
Assemble fragments into
contigs
Scaffolding– connecting
contigs usingmate-pair information
Slide5Steps involved in Illumina
Assembly
1) Download data (qseq file– sequences with quality scores)2) Filter dataA) Filter low quality readsB) 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
Slide62) Filtering data (specifics)
A) Remove low quality readsRemove 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 BioConductor ShortRead package (
may have to convert files from qseq to fastq
format)B) Remove adapter sequencesneed adapter sequence information from person that did sequencing Can use vectorstrip in EMBOSS
Slide7Computational power and
time required for
SOAPdenovo?Li et al 2010 Genome Research
Slide8And compared to other programs
Lin et al 2011
Genomics
Slide9Acromyrmex
echinatior genome raw data
NCBI: SRA Acromyrmex genome
Mate pair libraries(More redundant,
To build scaffolds)Shotgun libraries(Broader coverage, To build
contigs)
Slide10Slide11Paired end sequencing (<1Kb)
Mate pair library, paired end sequencing (>1Kb)