Whole Genome Sequencing and Assembly - SRA

SRX111329: Whole Genome Sequencing and Assembly
16 PACBIO_SMRT (PacBio RS) runs: 1.3M spots, 644.9M bases, 2.6Gb downloads

UUID: db80253d-5b59-469f-a0ad-e01023a29334

Design: Fragment library

Submitted by: Broad Institute (BI)

Study: Genome sequencing with short reads

PRJNA40077 • SRP001079 • All experiments • All runs

show Abstracthide Abstract

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_111_Rsphaeroides

Instrument: PacBio RS

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: SINGLE

Construction protocol: Pacific Biosciences

Spot descriptor:

1 forward

Experiment attributes: (show all 13 attributes...) (hide...)

gssr_id: 17970.36

lsid: BROAD:SEQUENCING_SAMPLE:17970.36

material_type: Genomic DNA

pacbio_rs_binding_kit: DNA/Polymerase Binding Kit 1.0 (24 rxn)

pacbio_rs_binding_kit_barcode: 110125001359802061511

pacbio_rs_template_prep_kit: DNA Template Prep Kit 1.0 (10 ug)

pacbio_rs_template_prep_kit_barcode: 110128001322716102811

project: D709

sequencing_protocol: Standard Sequencing

template_preparation_adaptor_sequence: ATCTCTCTCttttcctcctcctccgttgttgttgttGAGAGAGAT

template_preparation_kit_insert_size: 4100

used_binding_kit_control: true

work_request: 26267

Pipeline: show...hide...

Name	Step	Program	Version
2011-09-01 20:21:53.0	Instrument Control Version	1.2.1.0.87716
base caller	2011-09-02 02:23:15.0	Primary Analysis	NRT@172.31.128.10:8082, SwVer=1210.87716, HwVer=1.0

Runs: 16 runs, 1.3M spots, 644.9M bases, 2.6Gb

Run	# of Spots	# of Bases	Size	Published
SRR389110	81,741	38.3M	157.3Mb	2011-12-13
SRR389111	81,741	42.9M	176.4Mb	2011-12-13
SRR389112	81,741	53.1M	218.5Mb	2011-12-13
SRR389113	81,741	27.2M	108.7Mb	2011-12-13
SRR389114	81,741	42.6M	174.7Mb	2011-12-13
SRR389115	81,741	34.8M	141.3Mb	2011-12-13
SRR389116	81,741	40.8M	167.5Mb	2011-12-13
SRR389117	81,741	35.9M	145.7Mb	2011-12-13
SRR389118	81,741	38.5M	158.2Mb	2011-12-13
SRR389119	81,741	29.3M	119.1Mb	2011-12-13
SRR389120	81,741	40.4M	165.7Mb	2011-12-13
SRR389121	81,741	52.7M	215.7Mb	2011-12-13
SRR389122	81,741	37.2M	149.4Mb	2011-12-13
SRR389123	81,741	32.9M	133.3Mb	2011-12-13
SRR389124	81,741	43.9M	178.1Mb	2011-12-13
There are 1 omitted runs. See all runs in Run Selector.

ID:: 128773

SRA

Sequence Read Archive

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