Meet the ants

Camponotus floridanusCarpenter ant

Harpegnathos saltatorJumping ant Solenopsis invicta

Red imported fire ant

Pogonomyrmex barbatusHarvester ant

Linepithema humileArgentine ant

Atta cephalotes Acromyrmex echinatiorLeafcutter

ants

Now meet their genomes…

Species Citation Platform(Coverage)

Assembly Program(s)

Scaffold Length N50 (total)

Harpegnathos saltatorJumping ant

Bonasio et al 2010 Science

Illumina(104x)

SOAP de novo6 lib.- 3 paired end, 3 mate pair

598 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 ant

Nygaard et al 2011 Genome Research

Illumina(123x)

SOAP de novo5 lib.– 2 paired end, 3 mate pair

1.1 Mb(300Mb)

Atta cephalotesLeafcutter ant

Suen et al. 2011 PNAS

454(18-20x)

Roche GSAssembler

5.1 Mb(317 Mb)

Solenopsis invictaFire ant

Wurm et al. 2011 PNAS

454 + Illumina(~55x)

SOAP denovo + Roche GS Assembler

720 Kb(353 Mb)

Linepithema humileArgentine ant

Smith et al. 2011 PNAS

454 + Illumina(23x)

Roche GS Assembler + Celera CABOG

1.3 Mb(43 Mb)

Pogonomyrmex barbatusHarvester ant

Smith et al. 2011 PNAS

454(10-12x)

Celera CABOG 793 Kb(235 Mb)

Generic assembly procedure

Assemble fragments into contigs

Scaffolding– connecting contigs usingmate-pair information

Steps involved in Illumina Assembly

1) Download data (qseq file– sequences with quality scores)2) Filter data

A) Filter low quality readsB) Trim adapter sequences

3) SOAPdenovo stepsA) 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

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 BioConductor ShortRead 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

Computational power and time required for SOAPdenovo?

Li et al 2010 Genome Research

And compared to other programs

Lin et al 2011 Genomics

Acromyrmex echinatior genome raw dataNCBI: SRA Acromyrmex genome

Mate pair libraries(More redundant, To build scaffolds)

Shotgun libraries(Broader coverage, To build contigs)

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