Sequence Read Archive (SRA, Short Read Archive)

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

F1000Research ◽

10.12688/f1000research.9912.3 ◽

2016 ◽

Vol 5 ◽

pp. 2644 ◽

Cited By ~ 1

Author(s):

William P. Gilks ◽

Tanya M. Pennell ◽

Ilona Flis ◽

Matthew T. Webster ◽

Edward H. Morrow

Keyword(s):

Drosophila Melanogaster ◽

Complex Traits ◽

High Throughput Sequencing ◽

Population Sample ◽

Genomic Variation ◽

Genotype Data ◽

Whole Genome ◽

Short Read ◽

Short Read Archive ◽

Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

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Extensive horizontal exchange of transposable elements in the Drosophila pseudoobscura group

10.1101/284117 ◽

2018 ◽

Author(s):

Tom Hill ◽

Andrea J. Betancourt

Keyword(s):

Horizontal Transfer ◽

Species Group ◽

Data Availability ◽

Drosophila Pseudoobscura ◽

Chromosome Size ◽

Short Read ◽

Short Read Archive ◽

Ncbi Short Read Archive ◽

Mobile Component ◽

Different Levels

AbstractWhile the horizontal transfer of a parasitic element can be a potentially catastrophic, it is increasingly recognized as a common occurrence. The horizontal exchange, or lack of exchange, of TE content between species results in different levels of divergence among a species group in the mobile component of their genomes. Here, we examine differences in the TE content of the Drosophila pseudoobscura species group. We identify several putative horizontal transfer events, and examine the role that horizontal transfer plays in the spread of TE families to new species and the homogenization of TE content in these species. Despite rampant exchange of TE families between species, we find that both TE content differs hugely across the group, likely due to differing activity of each TE family and differing suppression of TEs due to divergence in Y chromosome size, and its resulting effects of TE regulation. Overall, we show that TE content is highly dynamic in this species group, and that it plays a large role in shaping the differences seen between species.Data availabilityAll data used in this study (summarized in table S1) is freely available online through the NCBI short read archive (NCBI SRA: ERR127385, SRR330416, SRR330418, SRR1925723, SRR330426, SRR330420, SRR330423, SRR617430-74). All genomes used are either available through flybase.org or popoolation.at.

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Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

10.1101/017087 ◽

2015 ◽

Cited By ~ 6

Author(s):

Brad Solomon ◽

Carleton Kingsford

Keyword(s):

Large Scale ◽

Rna Seq ◽

Large Collection ◽

Short Read ◽

Indexing Scheme ◽

Short Read Sequencing ◽

Sequence Read Archive ◽

Gene Isoform ◽

Expressed Sequence ◽

Novel Isoforms

Enormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequence Read Archive (SRA) are now available. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. A natural question is which of these experiments contain sequences that indicate the expression of a particular sequence such as a gene isoform, lncRNA, or uORF. However, at present this is a computationally demanding question at the scale of these databases. We introduce an indexing scheme, the Sequence Bloom Tree (SBT), to support sequence-based querying of terabase-scale collections of thousands of short-read sequencing experiments. We apply SBT to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2652 publicly available RNA-seq experiments contained in the NIH for the breast, blood, and brain tissues, comprising 5 terabytes of sequence. SBTs of this size can be queried for a 1000 nt sequence in 19 minutes using less than 300 MB of RAM, over 100 times faster than standard usage of SRA-BLAST and 119 times faster than STAR. SBTs allow for fast identification of experiments with expressed novel isoforms, even if these isoforms were unknown at the time the SBT was built. We also provide some theoretical guidance about appropriate parameter selection in SBT and propose a sampling-based scheme for potentially scaling SBT to even larger collections of files. While SBT can handle any set of reads, we demonstrate the effectiveness of SBT by searching a large collection of blood, brain, and breast RNA-seq files for all 214,293 known human transcripts to identify tissue-specific transcripts. The implementation used in the experiments below is in C++ and is available as open source at http://www.cs.cmu.edu/~ckingsf/software/bloomtree.

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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster

F1000Research ◽

10.12688/f1000research.9912.2 ◽

2016 ◽

Vol 5 ◽

pp. 2644

Author(s):

William P. Gilks ◽

Tanya M. Pennell ◽

Ilona Flis ◽

Matthew T. Webster ◽

Edward H. Morrow

Keyword(s):

Drosophila Melanogaster ◽

Complex Traits ◽

High Throughput Sequencing ◽

Genomic Variation ◽

Genotype Data ◽

Whole Genome ◽

Unique Haplotype ◽

Short Read ◽

Short Read Archive ◽

Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

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The Lair: A resource for exploratory analysis of published RNA-Seq data

10.1101/056200 ◽

2016 ◽

Author(s):

Harold Pimentel ◽

Pascal Sturmfels ◽

Nicolas Bray ◽

Páll Melsted ◽

Lior Pachter

Keyword(s):

Large Scale ◽

Exploratory Analysis ◽

Technical Expertise ◽

Rna Seq ◽

Sequencing Data ◽

Short Read ◽

Link Type ◽

Short Read Archive ◽

Published Research

AbstractIncreased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is typically not easily usable in practice. We introduce a series of tools for processing and analyzing RNA-Seq data in the Short Read Archive, that together have allowed us to build an easily extendable resource for analysis of data underlying published papers. Our system makes the exploration of data easily accessible and usable without technical expertise. Our database and associated tools can be accessed at The Lair: http://pachterlab.github.io/lair

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The complete genome sequences of two species of seventeen-year cicadas: Magicicada septendecim and Magicicada septendecula

F1000Research ◽

10.12688/f1000research.27309.1 ◽

2021 ◽

Vol 10 ◽

pp. 215

Author(s):

Harold B. White ◽

Stacy Pirro

Keyword(s):

North America ◽

Related Species ◽

De Novo ◽

Eastern North America ◽

Whole Genome ◽

Genome Sequences ◽

Short Read ◽

Short Read Archive ◽

Periodical Cicadas ◽

Ncbi Short Read Archive

The genus Magicicada (Hemiptera: Cicadidae) includes the periodical cicadas of Eastern North America. Spending the majority of their long lives underground, the adult cicadas emerge every 13 or 17 years to spend 4-6 weeks as adult to mate. We present the whole genome sequences of two species of 17-year cicadas, Magicicada septendecim and Magicicada septendecula. The reads were assembled by a de novo method followed by alignments to related species. Annotation was performed by GeneMark-ES. The raw and assembled data is available via NCBI Short Read Archive and Assembly databases.

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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

10.1101/081554 ◽

2016 ◽

Author(s):

William P. Gilks ◽

Tanya M. Pennell ◽

Ilona Flis ◽

Matthew T. Webster ◽

Edward H. Morrow

Keyword(s):

Drosophila Melanogaster ◽

Complex Traits ◽

Population Sample ◽

Genomic Variation ◽

Reference Line ◽

Genotype Data ◽

Whole Genome ◽

Short Read ◽

Short Read Archive ◽

Ncbi Short Read Archive

AbstractAs part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 2 females from the Berkeley reference line (BDGP6/dm6), and 220 hemiclonal females that were heterozygous for the same reference line genome, and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (BioProject PRJNA282591). Haplotype Caller discovered and genotyped 1,726,931 genetic variants (SNPs and indels, <200bp). Additionally, we used GenomeStrip/2.0 to discover and genotype 167 large structural variants (1-100Kb in size). Sequence data and quality-filtered genotype data are publicly-available at NCBI (Short Read Archive, dbSNP and dbVar). We have also released the unfiltered genotype data, and the code and logs for data processing, summary statistics, and graphs, via the research data repository, Zenodo, (https://zenodo.org/, ’Sussex Drosophila Sequencing’ community).

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