1343 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 the ta...1328 days ago
Applied Computational Genomics Course at UU: Spring 2020
This course will provide a comprehensive introduction to fundamental concepts and exper...al strategies. A diverse range of biological questions enabled by modern DNA sequencing technologies will be explored...1286 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.1283 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 the source package, you can find an executable file ktrim under bi...1235 days ago
307 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove false positives Calcula...d emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to...1220 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/bbab022/61467721205 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 pl...1101 days ago
QuasR: Quantification and annotation of short reads in R
The QuasR package (short for Quantify and annotate short reads in R) integrates the fun...package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from th...1053 days ago