Genome assembly software tools | De novo sequencing data analysis
Genome assembly is an obligatory step in de novo DNA sequencing, where long and short reads are put together to reconstitute a complete genome sequence. In de novo genome assembly, no reference genome is used, which renders the task more complex and time-consuming than mapping. De novo genome assembly software tools detect overlaps between reads, assemble overlaps into contigs, and then combine contigs into scaffolds in order to obtain a draft genome sequence.
Uses as a splice-aware aligner for short and long reads. BBTools is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations than others. It has particularly outstanding performance with deletions, especially long ones, that other aligners cannot handle at all. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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 genome assemblies. ALLPATHS-LG is a short‐read assembler that permits to generate high‐quality genome assemblies using short reads. This application is also able to perform de novo assembly of large mammalian genomes. The uncovered regions of the genome consist largely of repetitive sequences, with segmental duplications. It was developed to works with Illumina technology machines.
Conducts next generation sequencing (NGS) investigation. Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. It increases process efficiency and improves data organization. This tool enables the importation and conversion of a vast range of data types and offers a solution to customize researchers’ algorithms.