SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data,
as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate …
as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate …
Targeted sequence capture as a powerful tool for evolutionary analysis1
Next‐generation sequencing technologies (NGS) have revolutionized biological research by
significantly increasing data generation while simultaneously decreasing the time to data …
significantly increasing data generation while simultaneously decreasing the time to data …
Xenomapper: mapping reads in a mixed species context
MJ Wakefield - Journal of Open Source Software, 2016 - joss.theoj.org
Xenomapper is a utility for post processing mapped DNA sequencing reads that have been
aligned to a primary genome and a secondary genome, and binning reads into species …
aligned to a primary genome and a secondary genome, and binning reads into species …
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads
Background Sequencing of marker genes amplified from environmental samples, known as
amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate …
amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate …
A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics
P G. Ribeiro, MF Torres Jiménez… - Molecular …, 2021 - Wiley Online Library
The increasing availability of short‐read whole genome sequencing (WGS) provides
unprecedented opportunities to study ecological and evolutionary processes. Although loci …
unprecedented opportunities to study ecological and evolutionary processes. Although loci …
Comparison of short-read sequence aligners indicates strengths and weaknesses for biologists to consider
R Musich, L Cadle-Davidson, MV Osier - Frontiers in Plant Science, 2021 - frontiersin.org
Aligning short-read sequences is the foundational step to most genomic and transcriptomic
analyses, but not all tools perform equally, and choosing among the growing body of …
analyses, but not all tools perform equally, and choosing among the growing body of …
ReadTools: A universal toolkit for handling sequence data from different sequencing platforms
D Gómez‐Sánchez, C Schlötterer - Molecular ecology …, 2018 - Wiley Online Library
Sequencing whole genomes has become a standard research tool in many disciplines
including Molecular Ecology, but the rapid technological advances in combination with …
including Molecular Ecology, but the rapid technological advances in combination with …
IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries
Motivation 16S rDNA hypervariable tag sequencing has become the de facto method for
accessing microbial diversity. Illumina paired-end sequencing, which produces two separate …
accessing microbial diversity. Illumina paired-end sequencing, which produces two separate …
[HTML][HTML] Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
Target sequence capture has emerged as a powerful method to sequence hundreds or
thousands of genomic regions in a cost-and time-efficient approach. In most cases, however …
thousands of genomic regions in a cost-and time-efficient approach. In most cases, however …
New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics
Despite many bioinformatic solutions for analyzing sequencing data, few options exist for
targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate …
targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate …