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 …
Assembling and validating bioinformatic pipelines for next-generation sequencing clinical assays
JA SoRelle, M Wachsmann… - Archives of pathology …, 2020 - meridian.allenpress.com
… Clinical NGS results rely heavily on the bioinformatics pipeline for identifying genetic
variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and …
variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and …
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 …
VirAmp: a galaxy-based viral genome assembly pipeline
… and variation analysis limits the ability of individual labs to perform further bioinformatics …
contain smaller contigs compared to those obtained from overlap-layout-consensus algorithms. …
contain smaller contigs compared to those obtained from overlap-layout-consensus algorithms. …
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 …
Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool
JM Shelton, MC Coleman, N Herndon, N Lu, ET Lam… - BMC genomics, 2015 - Springer
… In this article we present software that leverages consensus genome maps assembled from
… Bioinformatics tools that could automate assembly editing based on such discrepancies are …
… Bioinformatics tools that could automate assembly editing based on such discrepancies are …