1345 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired...end Illumina Miseq data: raw amplicon sequencing data is processed into...of the DADA2 workflow identifies and v...tions of assigning taxonomy and assigning species to seque...1330 days ago
Applied Computational Genomics Course at UU: Spring 2020
This course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimenta...ectures covering key concepts and analytical strategies. A dive...iation, structural variation, and ChIP-seq and RNA-seq analysis. Stude...1288 days ago
FastProNGS: fast preprocessing of next-generation sequencing reads
FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.1284 days ago
Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing th...le ktrim under bin/ directory compiled using g++ v4.8.5 and linked...1237 days ago
309 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove...ncluding which filters to use and their thresholds) Option to...that is simple to both deploy and use, with filters and thresho...s and will slot into existing seque...efault variant caller outputs and performs better than other tools des...1222 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467721206 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and t...approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramil...1102 days ago
QuasR: Quantification and annotation of short reads in R
The QuasR package (short for Quantify and annotate short reads in R) integrate...ch as IRanges (Lawrence et al. 2013) and Rsamtools) and external softw...bowtie, through the Rbowtie package, and H...workflow of typical high throughput sequencing experiments, starting from th...1054 days ago