Cargando…

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment(1)

PREMISE OF THE STUDY: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of...

Descripción completa

Detalles Bibliográficos
Autores principales:	Johnson, Matthew G., Gardner, Elliot M., Liu, Yang, Medina, Rafael, Goffinet, Bernard, Shaw, A. Jonathan, Zerega, Nyree J. C., Wickett, Norman J.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Botanical Society of America 2016
Materias:	Software Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948903/ https://www.ncbi.nlm.nih.gov/pubmed/27437175 http://dx.doi.org/10.3732/apps.1600016

Ejemplares similares

Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery(1)
por: Gardner, Elliot M., et al.
Publicado: (2016)

hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution
por: Jackson, Chris, et al.
Publicado: (2023)

Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)
por: Gardner, Elliot M, et al.
Publicado: (2020)

SAMQA: error classification and validation of high-throughput sequenced read data
por: Robinson, Thomas, et al.
Publicado: (2011)

CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments
por: Uva, Paolo, et al.
Publicado: (2008)

Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data
por: Sadedin, Simon P., et al.
Publicado: (2019)

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
por: Falgueras, Juan, et al.
Publicado: (2010)

Short read sequence typing (SRST): multi-locus sequence types from short reads
por: Inouye, Michael, et al.
Publicado: (2012)

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
por: Parker, Matthew T., et al.
Publicado: (2021)

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees
por: Fér, Tomáš, et al.
Publicado: (2018)

VARUS: sampling complementary RNA reads from the sequence read archive
por: Stanke, Mario, et al.
Publicado: (2019)

GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining
por: Tong, W. M., et al.
Publicado: (2020)

iREAD: a tool for intron retention detection from RNA-seq data
por: Li, Hong-Dong, et al.
Publicado: (2020)

Taxonomic colouring of phylogenetic trees of protein sequences
por: Palidwor, Gareth, et al.
Publicado: (2006)

SAUTE: sequence assembly using target enrichment
por: Souvorov, Alexandre, et al.
Publicado: (2021)

Oculus: faster sequence alignment by streaming read compression
por: Veeneman, Brendan A, et al.
Publicado: (2012)

ChromaClade: combined visualisation of phylogenetic and sequence data
por: Monit, Christopher, et al.
Publicado: (2019)

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank
por: Abebe, Michael, et al.
Publicado: (2013)

SeqMaT: A sequence manipulation tool for phylogenetic analysis
por: Attaluri, Pavan Kumar, et al.
Publicado: (2011)

HALC: High throughput algorithm for long read error correction
por: Bao, Ergude, et al.
Publicado: (2017)

High-throughput sequence alignment using Graphics Processing Units
por: Schatz, Michael C, et al.
Publicado: (2007)

The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words
por: Kaczanowski, Szymon, et al.
Publicado: (2009)

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
por: Keller, Oliver, et al.
Publicado: (2008)

QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform
por: Shrestha, Ram Krishna, et al.
Publicado: (2014)

FastProNGS: fast preprocessing of next-generation sequencing reads
por: Liu, Xiaoshuang, et al.
Publicado: (2019)

InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data
por: Xiong, Wenwei, et al.
Publicado: (2013)

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
por: Leung, Elo, et al.
Publicado: (2016)

SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
por: Xia, Eryu, et al.
Publicado: (2016)

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
por: Francisco, Alexandre P, et al.
Publicado: (2012)

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees
por: Kedzierska, Anna M, et al.
Publicado: (2012)

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
por: Burdick, David B, et al.
Publicado: (2010)

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences
por: Bonizzoni, Paola, et al.
Publicado: (2005)

MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates
por: Delos Santos, Nathaniel P., et al.
Publicado: (2020)

TagDust2: a generic method to extract reads from sequencing data
por: Lassmann, Timo
Publicado: (2015)

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
por: Kluin, Roelof J. C., et al.
Publicado: (2018)

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data
por: Reddy, Shishir, et al.
Publicado: (2021)

PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets
por: Hong, Changjin, et al.
Publicado: (2015)

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
por: Wang, Wei-Chi, et al.
Publicado: (2009)

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing
por: Sato, Yukuto, et al.
Publicado: (2014)

DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data
por: Nettling, Martin, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_lhfu1i5peqma4di4hr4i1qh5re