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.

Assembles virus genomes from next generation sequencing (NGS) reads. VirusTAP is a web based platforms for the viral genome that performs the following informatics steps: (i) quality trimming and adaptor removal, (ii) read subtraction of host- and bacteria-related sequences by a read-mapping method, and (iii) de novo assembly using multiple combinations of recently advanced assemblers. It performs simple assembly using idba program.

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.

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.

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.

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.

Allows targeted de novo assembly and variance calling. NOVOLoci is a de novo local assembler that enables assembling of regions around set of genes or markers. The software can create a VCF file with all the detected variances, on condition that a reference is available.

Provides a scalable hierarchical multitasking parallel infrastructure with classical sequencing algorithms. PPSEQ offers parallel sequencing algorithms for genome indexing, sequence alignment, k-mer index builder, de novo assembly and detection of differential sequences between samples. It includes also a parallel indexer that builds an index from a set of DNA sequences and a parallel aligner that reads in both genome index files.