Targeted de novo assembly software tools | De novo sequencing data analysis

A computer program that conducts targeted local assembly of structural variants (SV) using targeted iterative graph routing assembly algorithm. Using data from the 1000 Genomes Project, TIGRA was able to accurately assemble the majority of deletion and mobile element insertion breakpoints, with a substantively better success rate and accuracy than other algorithms.

An in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data-mitochondrial baiting and iterative mapping. MITObim is capable of reconstructing mitochondrial genomes without the need of a reference genome of the targeted species by relying solely on (a) mitochondrial genome information of more distantly related taxa or (b) short mitochondrial barcoding sequences (seeds), such as the commonly used cytochrome-oxidase subunit 1 (COI), as a starting reference.MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24h using a standard desktop computer.

Uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. OSLay provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.

Uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector reconstructs introns and novel sequences within these loci, and scales well to large genomes – properties that makes it especially useful for researchers working on non-model eukaryotic organisms. It successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C. elegans and H. sapiens transcript targets in their corresponding genomic space using whole genome shot-gun (WGS) sequencing reads. The tool outperforms both established and recently released targeted assembly tools.

Assembles specific genomic regions from next-generation sequencing (NGS) data. GRAbB is a program using a reference file to identify reads corresponding to the target region. The software is designed to be flexible in terms of input options, assembly and completion criteria. It can handle multiple regions separately within a single run, and is also able to extract homologous sequence regions, such as barcoding sites. GRAbB can serve for extracting specific loci from NGS data, based on homology.