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PacBioCHM1_r2_GenBank_08152018

Organism name:
Homo sapiens (human)
BioSample:
SAMN02744161
BioProject:
PRJNA486145
Submitter:
McDonnell Genome Institute at Washington University
Date:
2018/08/31
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_001297185.2 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
LJII02
Assembly method:
PacBio Falcon v. 0.3+
Genome coverage:
60x
Sequencing technology:
PacBio; Illumina

IDs: 1912761 [UID] 7270598 [GenBank]

See Genome Information for Homo sapiens

There are 231 assemblies for this organism

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History (Show revision history)

Comment

Sequence Assembly Release Notes - Homo sapiens PacBioCHM1_r2_GenBank_08152018
 This is a contig-level assembly of the CHM1 genome. PacBioCHM1_r2_GenBank_08152018, is a draft and represents a work in progress. It will subsequently be re-submitted with additional scaffold and/or chromosome structure. These ... updates are expected within a few months of the initial submission date.
 Background:
 The CHM1 DNA for shotgun sequencing is derived from a human haploid hydatidiform mole. Sequence from this project will be used to improve the contiguity of the human reference sequence and add diverse allelic variation.
 Total sequence (subreads) input coverage on the PacBio instrument was 60X prior to error correction using a genome size estimate of 3Gb. The combined sequence reads were assembled using the Falcon software, and then error corrected using the Quiver algorithm. PacBioCHM1_r2_GenBank_08152018 is an updated version of GCA_001297185.1, which was previously submitted by Jason Chin at Pacbio. Pilon was run on the assembly and then contigs 200bp and less were removed. The assembly is made up of a total of 3709 contigs with an N50 contig length of 26.5Mb. The assembly spans 2.9Gb.
 This work was supported by the NHGRI 'IMPROVING THE HUMAN REFERENCE GENOME RESOURCE' grant no. 3U41HG007635.
 DNA Source Contact: Urvashi Surti Ph.D., Pittsburgh Cytogenetics Laboratory, University of Pittsburgh School of Medicine, Pittsburgh, PA.
 Homo sapiens CHM1_postPilon_1.0 Sequence and Assembly Credits:
 DNA source - Urvashi Surti Ph.D. Genome Sequence - LJII00000000.1; GCA_001297185.1 Sequence Assembly - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.

 Citation upon use of this assembly in a manuscript:
 It is requested that users of this H. sapiens PacBioCHM1_r2_GenBank_08152018 sequence assembly acknowledge McDonnell Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly. 

 Homo sapiens PacBioCHM1_r2_GenBank_08152018 assembly statistics: CONTIGS
 COUNT 3709
 LENGTH 2995735915
 AVG 807693
 N50 26898814 (26547048) 2613765
 LARGEST 109309871
 Contigs > 1M: 214 ( 2733057723 bp )
 Contigs 250K--1M: 165 ( 79546054 bp )
 Contigs 100K--250K: 391 ( 58176547 bp )
 Contigs 10K--100K: 2845 ( 124281824 bp )
 Contigs 5K--10K: 79 ( 612582 bp )
 Contigs 2K--5K: 15 ( 61185 bp )
 Contigs 0--2K: 0 ( 0 bp )  more

Global statistics

Total sequence length2,995,735,915
Total ungapped length2,995,735,915
Number of contigs3,709
Contig N5026,547,048
Contig L5030
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)3,709

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Contig
Count
Ungapped
Length
Contig
N50
Spanned
Gaps
Unspanned
Gaps
All2,995,735,9153,7092,995,735,91526,547,04800
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