Tools using SeqAn

Tools based on:

Seqan3

• Raptor - A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences
• iGenVar - A caller for all types of genetic variation: SNPs, indels and larger structural variations (insertions, deletions, inversions, translocations, CNVs, nested SVs). It uses both Illumina short reads and PacBio long reads for this purpose.
• Chopper - A tool for partitioning a set of sequences into similar batches.
• Lambda3 - The Local Aligner for Massive Biological DatA
• Needle - A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences
• Mars - Motif-based aligned RNA searcher
• Minions - Comparison between different methods to simplify sequence data
• RLM - Read level DNA methylation analysis of bisulfite converted sequencing data
• SeqAn3 Tools - Some helper tools/Demonstration of the library

Seqan2

• Lambda - The Local Aligner for Massive Biological DatA
• Lara - LaRA 2: Lagrangian Relaxed structural Alignment
• Vaquita - Identifies structural variations using split-reads, discordant read-pairs, soft-clipped reads, and read-depth information
• SLIMM - Species Level Identification of Microbes from Metagenomes
• Anise & Basil - Methods for the detection and assembly of novel sequence in high-throughput sequencing data