Targeted de novo assembly software tools | De novo sequencing data analysis
Production of high quality reference genome sequences for non-model organisms remains a challenging undertaking, especially for large (>1 Gbp) genomes. For such projects, de novo whole-genome assembly typically requires billions of sequencing reads from several different types of DNA libraries. An attractive alternative for generating reference sequences can be achieved through targeted assembly of gene/transcript sequences of interest. Even for species with scant transcriptomic sequence information, there are likely existing sequences that could be used to aid de novo assembly, such as homologous gene sequences from a related organism.
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.
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 genes using a single paired-end genomic library from divergent taxa assembles genes of interest. aTRAM is a software package inspired by the Target Restricted Assembly Method (TRAM). The software assembles genes of interest from short paired-end sequencing reads, including across divergent taxa by iteratively querying and assembling reads. It was used for assembling genes from highly divergent taxa from P. humanus.
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.
Processes large datasets of reads on commodity hardware. Mapsembler checks the presence of a known piece of information with a bounded number of substitutions in a set of reads. It provides pieces of information about the starter context(s), neighborhoods of approximate occurrences of a starter on some hundreds or thousands of nucleotides. The tool provides features like sub-starters retrieval, iterative extensions and graph visualization.
A genomics application that allows hypothesis-based interrogation of genomic regions (sequence targets) of interest. It only considers NGS reads for assembly that have overlap potential to input sequence targets.