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.
HipMer is a high-performance application that produces high-quality de novo assemblies for very large-scale genomes.
The MetaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions.
E. Georganas et al.,
“HipMer: an extreme-scale de novo genome assembler,”
SC ’15: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2015, pp. 1-11, doi: 10.1145/2807591.2807664.
Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K. Terabase-scale metagenome coassembly with MetaHipMer.
Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5. PMID: 32612216; PMCID: PMC7329831.
QUAST evaluates a quality of genome assemblies by computing various metrics and providing nice reports.
MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references.
Icarus is a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on QUAST genome quality assessment tool
