BOL: Related items

GenoViz: Visualization software for genomics

Rahul Nayak — Wed, 02 Jan 2019 04:07:57 -0600

GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our flagship product is Integrated Genome Browser (IGB).

For more information about IGB, visit http://bioviz.org.

Source code for the project was hosted here for many years. In 2014, we moved to a new git repository at http://www.bitbucket.org/lorainelab/integrated-genome-browser. We are still using SourceForge to distribute new releases of IGB as compiled code (igb.zip) you can use to run IGB on your computer.

If you have questions, feel free to get in touch. Contact project head Ann Loraine (aloraine@uncc.edu) or lead developer David Norris (dcnorris@uncc.edu>).

Address of the bookmark: https://sourceforge.net/projects/genoviz/

Troyanskaya Lab

Tue, 04 Feb 2020 06:40:36 -0600

The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets. We apply these approaches in studying challenging biological problems, such as how pathways function in diverse cell types and how they change dynamically.

https://function.princeton.edu/

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs

Surabhi Chaudhary — Sat, 25 Dec 2021 00:13:31 -0600

VCF2PopTree is a client-side software written in Javascript and it runs purely within the user’s computer/browser. VCF2PopTree is compatible with all population browsers including Chrome, Opera, Edge and Firefox and works equally efficient in Mac, Windows and Linux (Ubuntu).

Furthermore, it displays the tree in a mobile phone (iPhone and Android) if the input file size is small. CITATION: Subramanian, S., Ramasamy, U. and Chen, D. (2019). VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. Peer J. x:yy.

Address of the bookmark: https://github.com/sansubs/vcf2pop

dna2bit: an ultra-fast and accurate genomic distance estimation software

LEGE — Sun, 31 Aug 2025 06:24:58 -0500

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and MacOS platforms.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

Omega2: metagenome assembly pipeline

Jit — Mon, 10 Jul 2017 05:56:07 -0500

Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information. In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega provided comparable overall performance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison with Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a fraction of the computing time of existing overlap-layout-consensus assemblers. This indicates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for metagenomic datasets.

Address of the bookmark: http://omega.omicsbio.org/

RGFA: powerful and convenient handling of assembly graphs

Rahul Nayak — Thu, 25 Jan 2018 05:47:53 -0600

RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA.

https://github.com/ggonnella/rgfa

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103826/

MEC: Contig Misassembly Correction

BioStar — Tue, 04 Feb 2020 23:40:49 -0600

MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the statistical analysis of GC-contents. We apply MEC to four real contig datasets, and carry out experiments to analyze the influence of MEC on scaffolding results, which shows that MEC can reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available for download at https://github.com/bioinfomaticsCSU/MEC.

Address of the bookmark: https://github.com/bioinfomaticsCSU/MEC

SvABA: Structural variation and indel detection by local assembly

Jit — Tue, 10 Mar 2020 07:52:15 -0500

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.

Jit — Fri, 05 Feb 2021 21:22:24 -0600

GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

https://www.biorxiv.org/content/biorxiv/early/2021/02/01/2021.01.29.428779.full.pdf

Address of the bookmark: https://github.com/nadegeguiglielmoni/GraphUnzip

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Neel — Wed, 23 Jun 2021 07:54:53 -0500

LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116