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Protocols

DeepSeq specifications

Information


Unique identifier OMICS_19921
Name DeepSeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Hafeez Ur Rehman

Publication for DeepSeq

DeepSeq citations

 (16)
library_books

Conservation of a pH sensitive structure in the C terminal region of spider silk extends across the entire silk gene family

2018
Heredity
PMCID: 5943517
PMID: 29445119
DOI: 10.1038/s41437-018-0050-9

[…] RNA was extracted from the silk glands and whole abdomen of adult females and sequenced on an Illumina NextSeq500 (DeepSeq, University of Nottingham). Transcriptomes were trimmed using Scythe (Buffalo ) and Sickle (Joshi and Fass ) and assembled using Trinity (Grabherr et al. ). Protein sequences were predicted us […]

library_books

The peopling of the last Green Sahara revealed by high coverage resequencing of trans Saharan patrilineages

2018
Genome Biol
PMCID: 5809971
PMID: 29433568
DOI: 10.1186/s13059-018-1393-5

[…] g the current study are available in the dbSNP repository (https://www.ncbi.nlm.nih.gov/projects/SNP/) under accession numbers ss2137541472 and from ss3029944616 to ss3029952147 (handle, HUMGEN, ID Y_DEEPSEQ_2017) and are included in this published article (Additional file : Table S2). […]

library_books

H2AX facilitates classical non homologous end joining at the expense of limited nucleotide loss at repair junctions

2017
Nucleic Acids Res
PMCID: 5737864
PMID: 28977657
DOI: 10.1093/nar/gkx715

[…] After demultiplexing, forward and reverse paired-end reads were merged to generate a single consensus sequence per read pair using PEAR 0.9.8 (). Merged sequences were analyzed using the ‘DeepSeq Pipeline’, a self-analysis platform, which implemented a pairwise local sequence alignment algorithm called DBS-Aligner (Double Breakpoints Sequence Aligner) to align two genomic sequences wit […]

library_books

Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955

2017
Biotechnol Biofuels
PMCID: 5210280
PMID: 28066509
DOI: 10.1186/s13068-016-0692-x

[…] on from the strains DSM 2542, NCIMB 11955, TM89, TM242, NCIMB 11955ΔpyrE, LS003, LS004, TM89ΔpyrE and TM004. Paired-end libraries were prepared and sequenced (251 bp reads) using an Illumina MiSeq at DeepSeq, University of Nottingham. Preparation of paired-end libraries as well as sequencing was performed as described by the manufacturers. Reads were analysed using CLC Genomics Workbench and Artem […]

library_books

Complete Genome Sequence of Geobacillus thermoglucosidasius NCIMB 11955, the Progenitor of a Bioethanol Production Strain

2016
Genome Announc
PMCID: 5043570
PMID: 27688322
DOI: 10.1128/genomeA.01065-16

[…] ave sequenced the direct progenitor of TM242, NCIMB 11955.Genomic DNA was prepared using phenol-chloroform extraction. Paired-end libraries were sequenced using an Illumina MiSeq bench-top sequencer (Deepseq, University of Nottingham, Nottingham, UK), producing 1.66 Gb of data consisting of a total of 801,181,830 nucleotides (3,203,788 reads with an average length of 250.1 bp). Using CLC Genomics […]

library_books

What's a SNP between friends: The influence of single nucleotide polymorphisms on virulence and phenotypes of Clostridium difficile strain 630 and derivatives

2016
PMCID: 5626343
PMID: 27652799
DOI: 10.1080/21505594.2016.1237333

[…] +B-, 630E A+B-CT and 630Δerm A+B- was prepared by phenol:chloroform extraction. 630E A+B-, 630E A+B-CT, 630Δerm(ΔpyrE) were sequenced on Ilumina HiSeq (GATC, Germany) and 630Δerm A+B- on a Roche 454 (Deepseq, Nottingham, UK) and the data compared to the published genome of 630 using CLC genomic workbench. All raw sequencing data have been deposited in the sequence read archive (SRA) under the stud […]


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DeepSeq institution(s)
Max Planck Institute for Software Systems, Saarbrucken, Germany; FAST National University of Computer and Emerging Sciences, Peshawar, Pakistan; Department of Computer & Control Engineering, Politecnico di Torino, Torino, Italy
DeepSeq funding source(s)
Supported by Grant Number: 21-915/SRGP/R&D/HEC/2016 by the HEC; the contribution of a Tesla K40 GPU by NVIDIA Corporation.

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