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

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.

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.

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.

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.

A software for the targeted de novo assembly of genomic sequence from large-scale genomic or metagenomic datasets. PRICE is designed with paired-end data in mind but does not require such data. The features of the underlying software system can be used through two executables: 1) the full assembler, PriceTI, or 2) an executable for independently filtering read data prior to assembly, PriceSeqFilter.