Reference-assisted assembly software tools | De novo genome sequencing data analysis
An alternative approach for scaffolding genomes relies on the use of a complete (closed) reference genome to guide the ordering and the orientating of the contigs. Many available methods exist for mapping (and then scaffolding) the generated draft contigs.
Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles individual transcripts from RNA-seq reads that have been aligned to the genome. This software is able to infer the splicing structure of each gene because reads from multiple splice variants for a given gene can be found in a sample. Quantification of transcript abundances is also possible by preferring a reference annotation to assembling the reads.
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.
Assists users with DNA sequence analysis. Sequencher is a graphical application that integrates the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. It can generate unique data visualizations using customized plots and graphs that produces ready-to-print graphs. This model also includes an extensive Sanger analysis features.
Permits users to perform contig editing, mutation detection, or sequence assembly. CodonCode Aligner contains several characteristics allowing researchers to execute the following action: sequence editing and trimming, sequence alignment, sequence translation, restriction mapping, or primer design. This program also contains features for phylogenetic trees and methylation analysis.
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.
It is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated.
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.