Whole Genome Sequencing and Assembly - SRA

SRX109818: Whole Genome Sequencing and Assembly
4 PACBIO_SMRT (PacBio RS) runs: 242,668 spots, 89.1M bases, 347.4Mb downloads

UUID: 6d4955d7-4419-414b-957b-f2eabfe339f4

Design: Fragment library

Submitted by: Broad Institute (BI)

Study: Genome sequencing with short reads

PRJNA40077 • SRP001079 • All experiments • All runs

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To test methods for assembly of very short reads, five microbial genomes were selected which have a finished reference sequence available. Rhodobacter sphaeroides 2.4.1 was one of these five microbial genomes. At least two libraries (short fragment and jumping) were generated and sequenced using Illumina. Genomic DNA from Baylor. Two different genome assemblies are part of this project. The assembly in AKBU00000000 is from Illumina reads and contains 2 complete chromosomes, 3 complete plasmids and 2 incomplete plasmids that share long perfect overlaps, so are present as 6 contigs. The assembly in AKVW00000000 is from sequences in BioProject PRJNA56 plus reads from a different isolate of the strain. It contains 2 complete chromosomes and 5 complete plasmids, but the plasmid sequences differ from those in the genome assembled in BioProject PRJNA56.

Sample: Generic sample from Rhodobacter sphaeroides 2.4.1

SAMN00103269 • SRS004883 • All experiments • All runs

Organism: Cereibacter sphaeroides 2.4.1

Library:

Name: LR_12_Rsphaeroides

Instrument: PacBio RS

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: SINGLE

Construction protocol: Pacific Biosciences

Spot descriptor:

1 forward

Experiment attributes: (show all 12 attributes...) (hide...)

gssr_id: 17970.27

lsid: BROAD:SEQUENCING_SAMPLE:17970.27

material_type: Genomic DNA

pacbio_rs_binding_kit: DNA/Polymerase Binding Kit (24 rxn)

pacbio_rs_binding_kit_barcode: 100728000325953112610

pacbio_rs_template_prep_kit: DNA Template Prep Kit (8 rxn)

pacbio_rs_template_prep_kit_barcode: 100727000640391102210

project: G14221

sequencing_protocol: Standard Sequencing

template_preparation_adaptor_sequence: ATCTCTCTCttttcctcctcctccgttgttgttgttGAGAGAGAT

used_binding_kit_control: true

work_request: 27893

Pipeline: show...hide...

Name	Step	Program	Version
2010-10-07 14:12:10.0	Instrument Control Version	1.0.2.64758
base caller	2010-10-07 20:08:03.0	Primary Analysis	NRT@172.31.128.10:8082, SwVer=102.64758, HwVer=1.0

Runs: 4 runs, 242,668 spots, 89.1M bases, 347.4Mb

Run	# of Spots	# of Bases	Size	Published
SRR386600	60,667	27.2M	104.9Mb	2011-12-01
SRR386744	60,667	20M	78.4Mb	2011-12-01
SRR386745	60,667	17.6M	69.4Mb	2011-12-01
SRR386746	60,667	24.4M	94.7Mb	2011-12-01

ID:: 127095

SRA

Sequence Read Archive

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