Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Dries Decap"'
Autor:
Charlotte Herzeel, Pascal Costanza, Dries Decap, Jan Fostier, Roel Wuyts, Wilfried Verachtert
Publikováno v:
PLoS ONE, Vol 16, Iss 2, p e0244471 (2021)
We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and
Externí odkaz:
https://doaj.org/article/c98447a9b2c44f2790dc794e38772bb0
Publikováno v:
PLoS ONE, Vol 14, Iss 2, p e0209523 (2019)
We present elPrep 4, a reimplementation from scratch of the elPrep framework for processing sequence alignment map files in the Go programming language. elPrep 4 includes multiple new features allowing us to process all of the preparation steps defin
Externí odkaz:
https://doaj.org/article/bda0ea80751f403986c770b651ecce0c
Publikováno v:
PLoS ONE, Vol 12, Iss 3, p e0174575 (2017)
Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant
Externí odkaz:
https://doaj.org/article/7afe81e35d904e68963e4f90df48940a
Publikováno v:
PLoS ONE, Vol 10, Iss 7, p e0132868 (2015)
elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, re
Externí odkaz:
https://doaj.org/article/3320af9768664f5d8c6b531784bad2bf
Publikováno v:
DNA RESEARCH
With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site iden
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4efe67cc646c21e14db80c57e06f6070
https://lirias.kuleuven.be/handle/20.500.12942/700344
https://lirias.kuleuven.be/handle/20.500.12942/700344
Autor:
Dries Decap, Louise de Schaetzen van Brienen, Maarten Larmuseau, Pascal Costanza, Charlotte Herzeel, Roel Wuyts, Kathleen Marchal, Jan Fostier
Publikováno v:
GigaScience
GIGASCIENCE
GIGASCIENCE
Background The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-freq
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::44f58e1ec9c810706980192b079cf498
https://lirias.kuleuven.be/handle/20.500.12942/704379
https://lirias.kuleuven.be/handle/20.500.12942/704379
Autor:
Dries De Maeyer, Toon Swings, Jan Michiels, Dries Decap, Bram Weytjens, Camilo Andres Perez-Romero, Kathleen Marchal
Publikováno v:
NUCLEIC ACIDS RESEARCH
Nucleic Acids Research
Nucleic Acids Research
IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9d478c5b65463545e97d0d710b64521c
https://doi.org/10.1093/nar/gkz451
https://doi.org/10.1093/nar/gkz451
We present elPrep 4, a reimplementation from scratch of the elPrep framework for processing sequence alignment map files in the Go programming language. elPrep 4 includes multiple new features allowing us to process all of the preparation steps defin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4768b5ade6df50196b0c24d2db9ab5c8
https://doi.org/10.1101/492249
https://doi.org/10.1101/492249
Autor:
Dieter De Witte, Pieter Audenaert, Bart Dhoedt, Jan Van de Velde, Michiel Van Bel, Klaas Vandepoele, Dries Decap, Piet Demeester, Jan Fostier
Publikováno v:
Bioinformatics
BIOINFORMATICS
BIOINFORMATICS
Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1b5591d4100ce942779167410d80bc8
https://doi.org/10.1093/bioinformatics/btv466
https://doi.org/10.1093/bioinformatics/btv466
Publikováno v:
BIOINFORMATICS
Bioinformatics
Bioinformatics
Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine. R
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17294d5445442734f44f1f145b417989
https://doi.org/10.1093/bioinformatics/btv179
https://doi.org/10.1093/bioinformatics/btv179