HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
PT Truong Nguyen, I Plyusnin, T Sironen… - … bioinformatics, 2021 - Springer
… , which could perform fast reference-based assemblies on … bioinformatic pipeline called
HAVoC (Helsinki university Analyzer for Variants of Concern). HAVoC can reference assemble …
HAVoC (Helsinki university Analyzer for Variants of Concern). HAVoC can reference assemble …
VPipe: An automated bioinformatics platform for assembly and management of viral next-generation sequencing data
… ), an automated bioinformatics pipeline optimized for whole-genome assembly of viral
sequences … For the reference-based assembly of SARS-CoV-2, VPipe generated 22 consensus …
sequences … For the reference-based assembly of SARS-CoV-2, VPipe generated 22 consensus …
Bioinformatic data processing pipelines in support of next‐generation sequencing‐based HIV drug resistance testing: the Winnipeg consensus
… Although the functionalities and assembly of bioinformatics strategies applied in different …
Consensus on bioinformatic strategies for NGS HIVDR data processing. This consensus may …
Consensus on bioinformatic strategies for NGS HIVDR data processing. This consensus may …
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
… We report the optimization of circular consensus sequencing (CCS) to … De novo genome
assembly using CCS reads alone … outperforming assembly with less-accurate long reads. …
assembly using CCS reads alone … outperforming assembly with less-accurate long reads. …
The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing
… on to the consensus. Therefore, there is a need for consensus polishing for assemblies
produced … A base-level correction-free assembly pipeline is developed by directly analyzing and …
produced … A base-level correction-free assembly pipeline is developed by directly analyzing and …
SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
… During reference-based assembly (secapr reference_assembly) we mapped the reads
against the consensus sequence of the contig MSAs for all loci. We found an average of 454 …
against the consensus sequence of the contig MSAs for all loci. We found an average of 454 …
[HTML][HTML] Recommendations for the use of in silico approaches for next-generation sequencing bioinformatic pipeline validation: a joint report of the Association for …
EJ Duncavage, JF Coleman, ME de Baca… - The Journal of Molecular …, 2023 - Elsevier
… Such data allow laboratories to more accurately test the performance of clinical bioinformatics
pipelines without sequencing additional cases. For example, clinical laboratories may use …
pipelines without sequencing additional cases. For example, clinical laboratories may use …
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
JA Frank, Y Pan, A Tooming-Klunderud, VGH Eijsink… - Scientific reports, 2016 - nature.com
… DNA assembly is a core methodological step in metagenomic pipelines used to study the …
and/or proteins with novel functions that cannot be recognized by bioinformatics alone. …
and/or proteins with novel functions that cannot be recognized by bioinformatics alone. …
Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries
… A bootstrap analysis showed that the C3S-LAA pipeline per se was effective at removing
bioinformatic sources of error, but in rare cases a read depth of nearly 400X was not sufficient to …
bioinformatic sources of error, but in rare cases a read depth of nearly 400X was not sufficient to …
Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data
… Each of these frameworks can be used to build bioinformatics pipelines, to execute complex
tasks through the integration of software tools and the control of execution flow, in order to …
tasks through the integration of software tools and the control of execution flow, in order to …