Cargando…

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural vari...

Descripción completa

Detalles Bibliográficos
Autores principales:	Leggett, Richard M., Clavijo, Bernardo J., Clissold, Leah, Clark, Matthew D., Caccamo, Mario
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519/ https://www.ncbi.nlm.nih.gov/pubmed/24297520 http://dx.doi.org/10.1093/bioinformatics/btt702

Ejemplares similares

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs
por: Murphy, Rebecca R., et al.
Publicado: (2015)

Improved workflows for high throughput library preparation using the transposome-based nextera system
por: Lamble, Sarah, et al.
Publicado: (2013)

Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction
por: Gaio, Daniela, et al.
Publicado: (2022)

Assessment of insert sizes and adapter content in fastq data from NexteraXT libraries
por: Turner, Frances S.
Publicado: (2014)

X-MATE: a flexible system for mapping short read data
por: Wood, David L. A., et al.
Publicado: (2011)

AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries
por: Criscuolo, Alexis, et al.
Publicado: (2014)

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data
por: Zeitouni, Bruno, et al.
Publicado: (2010)

Swan: a library for the analysis and visualization of long-read transcriptomes
por: Reese, Fairlie, et al.
Publicado: (2020)

htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets
por: Sahadevan, Sudeep, et al.
Publicado: (2022)

HI: haplotype improver using paired-end short reads
por: Long, Quan, et al.
Publicado: (2009)

NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles
por: Leggett, Richard M., et al.
Publicado: (2016)

girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
por: Toedling, Joern, et al.
Publicado: (2010)

REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data
por: McLaughlin, Russell Lewis
Publicado: (2020)

Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination
por: Van Nieuwerburgh, Filip, et al.
Publicado: (2012)

YeastMate: neural network-assisted segmentation of mating and budding events in Saccharomyces cerevisiae
por: Bunk, David, et al.
Publicado: (2022)

AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs
por: Gorjanc, Gregor, et al.
Publicado: (2018)

Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)(1)
por: Beck, James B., et al.
Publicado: (2015)

Peakhood: individual site context extraction for CLIP-seq peak regions
por: Uhl, Michael, et al.
Publicado: (2021)

Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries
por: Srivastava, Anuj, et al.
Publicado: (2014)

Improving draft genome contiguity with reference-derived in silico mate-pair libraries
por: Grau, José Horacio, et al.
Publicado: (2018)

Read trimming is not required for mapping and quantification of RNA-seq reads at the gene level
por: Liao, Yang, et al.
Publicado: (2020)

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
por: Hunt, Martin, et al.
Publicado: (2022)

Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites
por: Her, Hsuan-Lin, et al.
Publicado: (2022)

The Sleipnir library for computational functional genomics
por: Huttenhower, Curtis, et al.
Publicado: (2008)

The systems biology simulation core library
por: Panchiwala, Hemil, et al.
Publicado: (2021)

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
por: Mapleson, Daniel, et al.
Publicado: (2017)

multiclassPairs: an R package to train multiclass pair-based classifier
por: Marzouka, Nour-Al-Dain, et al.
Publicado: (2021)

Aggressive assembly of pyrosequencing reads with mates
por: Miller, Jason R., et al.
Publicado: (2008)

NGSNGS: next-generation simulator for next-generation sequencing data
por: Henriksen, Rasmus Amund, et al.
Publicado: (2023)

COSMOS: Python library for massively parallel workflows
por: Gafni, Erik, et al.
Publicado: (2014)

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
por: Cloonan, Nicole, et al.
Publicado: (2009)

Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales
por: De La Cerda, Gisel Y., et al.
Publicado: (2023)

JSBML: a flexible Java library for working with SBML
por: Dräger, Andreas, et al.
Publicado: (2011)

The GNAT library for local and remote gene mention normalization
por: Hakenberg, Jörg, et al.
Publicado: (2011)

Bioclojure: a functional library for the manipulation of biological sequences
por: Plieskatt, Jordan, et al.
Publicado: (2014)

MuWU: Mutant-seq library analysis and annotation
por: Stöcker, Tyll, et al.
Publicado: (2021)

Chemsearch: collaborative compound libraries with structure-aware browsing
por: Gaffney, Stephen G, et al.
Publicado: (2021)

Mate-pair editing: a perspective to double mate-pair sequencing coverage
por: Jighly, Abdulqader
Publicado: (2016)

Updates to the RMAP short-read mapping software
por: Smith, Andrew D., et al.
Publicado: (2009)

Bathometer: lightning fast depth-of-reads query
por: Stenzel, U, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_cq18m10vu5n70n2ciovevpjhl4