grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories.

08:00 EDT 10th March 2020 | BioPortfolio

Summary of "grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories."

High-throughput sequencing is a powerful technique for addressing biological questions. Grabseqs streamlines access to publicly available metagenomic data by providing a single, easy-to-use interface to download data and metadata from multiple repositories including the Sequence Read Archive (SRA), the Metagenomics Rapid Annotation through Subsystems Technology (MG-RAST) server, and iMicrobe. Users can download data and metadata in a standardized format from any number of samples or projects from a given repository with a single grabseqs command.


Journal Details

This article was published in the following journal.

Name: Bioinformatics (Oxford, England)
ISSN: 1367-4811


DeepDyve research library

PubMed Articles [9311 Associated PubMed Articles listed on BioPortfolio]

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes.

The 3T3-L1 pre-adipocyte cell line is widely used to study the fat cell differentiation . Researchers also use this cell model to study obesity and insulin resistance. We surveyed the literature, the ...

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm.

Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs (bp). These long reads are used to construct an assembly (i.e., the subject's genome), whi...

A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads.

RNA sequencing (RNA-seq) is widely used to study gene-, transcript-, or exon expression. To quantify the expression level, millions of short sequenced reads need to be mapped back to a reference genom...

EPGA-SC : A framework for de novo assembly of single-cell sequencing reads.

Assembling genomes from single-cell sequencing data is essential for single-cell studies. However, single-cell assemblies are challenging due to (i) the highly non-uniform read coverage and (ii) the e...

BioSeqZip: a collapser of NGS redundant reads for the optimisation of sequence analysis.

High-Throughput Next-Generation-Sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resourc...

Clinical Trials [5467 Associated Clinical Trials listed on BioPortfolio]

Effectiveness of the Husky Reads Program to Increase Fruit and Vegetable Preference and Food Group Identification in Preschool Children

Since 1998, UCONN undergraduate students have volunteered as part of a service- learning course to deliver a program called Husky Reads. Inspired by the nationally accepted American Academ...

CT and Radiologist RCT

The use of computed tomography (CT) imaging is rapidly increasing in healthcare. Despite physicians' growing reliance on radiological assessments, however, the reliability and accuracy of ...

The Results of Multiple Aspirations and Injections of Unicameral Bone Cyst by Methyl Prednisolone Acetate

Evaluation of the efficacy of methyl prednisolone injection in treatment o f simple bone cyst to prevent all possible complications as pathological fractures and to avoid prolonged restric...

Simple Suppers Scale-up (S3)

The purpose of this study is to determine effectiveness of a family meals intervention, Simple Suppers, aimed at eliciting positive changes in child dietary intake and weight status.

Stage I Multiple Myeloma Treatment

- Assessment of survival without progression of stage I MM in two groups: arm A: simple survey and arm B: administration of Zoledronate. - Describe different progression's type ...

Medical and Biotech [MESH] Definitions

Structured data elements used to describe other data.

Lists of material available in a library arranged in order with bibliographical METADATA for the purpose of identification and retrieval.

A fibrosarcoma of the skin, beginning most often as an indurated nodule that grows slowly and hence is often ignored until it grows large. Dermatofibrosarcomas show an extremely aggressive tendency to invade local surrounding tissue. They do not metastasize, however, even after multiple recurrences. About 50% will recur after simple incision; hence wide excision should be resorted to. (DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, p1356)

The offspring in multiple pregnancies (PREGNANCY, MULTIPLE): TWINS; TRIPLETS; QUADRUPLETS; QUINTUPLETS; etc.

A form of multiple sclerosis characterized by a progressive deterioration in neurologic function which is in contrast to the more typical relapsing remitting form. If the clinical course is free of distinct remissions, it is referred to as primary progressive multiple sclerosis. When the progressive decline is punctuated by acute exacerbations, it is referred to as progressive relapsing multiple sclerosis. The term secondary progressive multiple sclerosis is used when relapsing remitting multiple sclerosis evolves into the chronic progressive form. (From Ann Neurol 1994;36 Suppl:S73-S79; Adams et al., Principles of Neurology, 6th ed, pp903-914)

Quick Search

DeepDyve research library

Relevant Topics

DNA sequencing
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...

Searches Linking to this Article