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...1329 days ago
Applied Computational Genomics Course at UU: Spring 2020
...ategies. A diverse range of biological questions enabled by modern DNA sequencing technologies will be e...ification of genetic variation, structural variation, and ChIP-seq and RNA-seq analysis. Students will learn an...1287 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
1256 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...1236 days ago
308 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove false positives Ca...and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to...1221 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
IVA: accurate de novo assembly of RNA virus genomes
IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus...1105 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...1102 days ago