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.
Assembles data from Sanger sequencer such as ABI, 454 and Illumina next-generation sequencers. ChromasPro is designed to assemble sequence reads into contigs, with a graphical contig editor displaying aligned chromatograms. The software also enables general sequence analysis such as restriction enzyme mapping, open-reading-frame (ORF) searches, and BLAST submission.
Corrects draft assemblies and calls sequence variants of multiple sizes, including very large insertions and deletions. Pilon improves draft genome assemblies by correcting bases, fixing miss-assemblies and filling gaps. In addition, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions.
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.