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Mugsy: multiple whole genome alignment tool
By Jit 3011 days ago Comments (1)mugsy.sourceforge.net - Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee....GIGGLE: a search engine for large-scale integrated genome analysis
By Jit 2979 days agogithub.com - GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is...GenomeTools: The versatile open source genome analysis software
By Jit 2951 days agohttp://genometools.org/ - The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 2882 days agogithub.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2827 days agoderisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...Converting a VCF into a FASTA given some reference !
By Jit 2788 days agoconverting a VCF file into a FASTA file given a reference sequenceHaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome...
By BioStar 2719 days agogithub.com - HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a...QUAST-LG: Versatile genome assembly evaluation
By Jit 2691 days agocab.spbu.ru - QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we...Genobuntu: A software package containing more than 70 software and packages oriented towards NGS...
By BioStar 2644 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological...CANU genome assembly parameters !
By Rahul Nayak 2617 days agoChoose the appropriate parameters to run Canu and run it.
