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SPAdes
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A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide Additional contigs can also be provided to be used as long reads. SPAdes supports paired-end reads, mate-pairs and unpaired reads and can take as input several paired-end and mate-pair libraries simultaneously.
MITObim / MITOchondrial Baiting and Iterative Mapping
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.
r2cat / related reference contig arrangement tool
It is able to quickly match a set of contigs onto a related genome, order the contigs according to their matches and display the result in an interactive synteny plot. The matching, however, is not restricted to contigs, such that the program can also be used to visualize the synteny of two finished genomes. The software is open source and available within the Comparative Genomics – Contig Arrangement Toolsuite (CG-CAT) on the Bielefeld Bioinformatics Server (BiBiServ).
Ragout / Reference-Assisted Genome Ordering UTility
A tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the contigs into scaffolds. The benefits of assembly with multiple references become significant, when those references have structural variations compared to the target genome. Even if each reference is structurally divergent, it is possible to assemble the target into the correct set of scaffolds.
AlignGraph
An algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. AlignGraph aligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph. The incorporated positional information from the alignments and PE reads allows you to extend the initial assemblies, while avoiding incorrect extensions and early terminations.
HaploMerger
Improves genome assembly in the post-assembly stage. HaploMerger is an automated pipeline to resolve allelic relations in polymorphic diploid assembly and output the reference haploid assembly. It can work with both heterozygosity-aware and -unaware genome assemblers and process both low and high heterozygosity assemblies. It can work on pre-existing diploid assemblies and is easily incorporated into any assembly pipelines. A major upgrade permits to reconstruct both haploid subassemblies from short-read and long-read diploid assemblies.
BAUM
Allows users to perform reference-assisted assembly or improve genome assembly based on second generation sequencing (SGS) paired-end/mate-pair libraries. BAUM is composed of two modules allowing users to construct: (1) the genome unique regions, which are taken as the initial contigs; and (2) iterative assembly aiming to reconstruct the repetitive regions along the iterations. This tool can be applied to test different eukaryote genomes, such as a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus.
CAR / Contig Assembly of prokaryotic draft genomes using rearrangements
A reference-based contig assembly (or scaffolding) tool that can efficiently and more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome of a related organism. Given a set of contigs in multi-FASTA format and a reference genome in FASTA format, CAR can output a list of scaffolds, each of which is a set of ordered and oriented contigs. For validation, CAR has been tested on a real dataset composed of several prokaryotic genomes and also compared its performance with several other reference-based contig assembly tools.
Multi-CAR
Orders and orients the contigs of a draft genome by using multiple complete genomes of related organisms as references. Multi-CAR was tested on a real dataset composed of several prokaryotic genomes. The tool was able to finish its contig scaffolding job in several seconds up to a couple of minutes. The returned accurate scaffolds of the draft genome can reduce the cost of production of high-quality complete genome, so the tool appears to be very useful for the research community.
DeNoGAP / De-Novo Genome Analysis Pipeline
Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of Genomes. It scales linearly since the homology assignment is based on iteratively refined hidden Markov models. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences.
CONTIGuator
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Designed for the bacterial genomes finishing process. CONTIGuator is a software that combines the routines of ABACAS with a contig profiling viewable with the Artemis comparison tool. The software provides Polymerase Chain Reaction (PCR) primers set to close more gaps and gives clues on the relative position of various contigs. Contigs profiling provides a high-resolution map, highlighting regions of the reference genomes that are diverging from assembled contigs. CONTIGuator allows investigation of the structural genomics based on draft genome sequences.
NovoAlign
Uses for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms. NovoAlign is packed with unsurpassed features like alignment quality scores using posterior alignment probability, mismatches and gaps of up to 50% of read length, automatic base quality calibration and many others. Benchmarks shows that NovoAlign3 performed better in all the aspect of alignment, with higher total correct mapped, and significantly lower incorrectly mapped reads.
RACA / Reference-Assisted Chromosome Assembly
Obsolete
An algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that RACA can substantially improve genomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely related species and outgroup genomes are available.
HighMap
Constructs high-density linkage maps from next-generation sequencing (NGS) data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. HighMap consists of four modules, designed for linkage grouping, marker ordering, error genotyping correction and map evaluation. It is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL (Quantitative Trait Locus) studies.
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