PAVFinder is a Python package that detects genomic rearrangements from whole-genome shotgun assemblies and transcriptomic events such as gene fusions, internal tandem duplications, partial tandem duplications, and novel splice variants from RNA-seq assemblies.
ntJoin is an assembly-guided scaffolder which uses a lightweight, alignment-free mapping strategy in lieu of alignments to quickly contiguate a target assembly using one or more
SAT-Assembler can perform targeted gene assembly for both RNA-Seq and metagenomic data. It addresses the above challenges of de novo assembly of large scale NGS data by conducting family-specic gene assembly, homology-guided overlap graph construction, and careful graph traversal.
fq2dna is a command line tool to ease the de novo assembly of archaea, bacteria or virus genomes from raw high-throughput sequencing (HTS) paired-end (PE) reads.