Good Resource To Learn About 'Smaller' De Novo Eukaryotic Genome Assembly

Question

[Travis]

Hi all,

I am wondering if there are any resources out there that might provide a good good overview of genome assembly (specifically eukaryotic, 300-400 MB). No data yet exists for this, and it is very new to me.

Thanks in advance.

Answer 1

[Rm]

Look for published assembled genomes published, see the methods, supplemental data files and corresponding read deposits in SRA

http://www.ncbi.nlm.nih.gov/sra?term=srr001666

De Novo Assembly of Illumina reads with Velvet (1.0.17) and read alignment with Bowtie (0.12.7)

http://www.ebi.ac.uk/training/ftp/private/onsite/NGS_April/day2_velvet_tutorial_1.pdf

http://www.ebi.ac.uk/training/ftp/private/onsite/NGS_April/day2_velvet_tutorial_2.pdf

http://www.ebi.ac.uk/training/ftp/private/onsite/NGS_April/day2_velvet_tutorial_3.pdf

My bad, missed Eukaryotic part.

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

Data access

"Raw read data are available through NCBI genome project ID 39847: fosmid PE Sanger reads (see Additional data file 2 for a complete list of accessions); SE 454 reads [SRA:SRR023307] and [SRA:SRR023517] to [SRA:SRR023533]; 200 bp PE Illumina reads [SRA:SRR018008] to [SRA:SRR018011] and 700 bp PE Illumina reads [SRA:SRR018012]. Assemblies have also been deposited at NCBI: Sanger-454-IlluminaPA [DDBJ/EMBL/GenBank:ACXQ00000000]; Sanger-454-IlluminaDA [DDBJ/EMBL/GenBank:ACYC00000000]."

http://www.ncbi.nlm.nih.gov/sra/SRX007346

http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP004761