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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (310 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (767 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (928 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (980 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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By Rahul Agarwal 1892 days agobioinformatik.de - FaBI emerged from the respective groups of the four founding societies GI (German Informatics Society), DECHEMA (Society for Chemical Engineering and Biotechnology), GBM (Society for Biochemistry and Molecular Biology) and GDCh (German Chemical...The Global Alliance for Genomics and Health (GA4GH)
By Jit 1893 days agohttps://www.ga4gh.org/ - The Global Alliance for Genomics and Health (GA4GH) is a policy-framing and technical standards-setting organization, seeking to enable responsible genomic data sharing within a human rights framework. GA4GH core funders and sponsors enable our...Bio7: an integrated development environment for ecological modeling, scientific image analysis and...
By Nidhi Rajput 1893 days agohttps://bio7.org/home-2/ - The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge...Free Genomics data !
By BioStar 1893 days agowww.darwintreeoflife.org - The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane...Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 1894 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...shinyCircos: an R/Shiny application for interactive creation of Circos plot
By Jit 1894 days ago150.109.59.144 - shinyCircos, a graphical user interface for interactive creation of Circos plot. shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community. Furthermore, various...MEC: Contig Misassembly Correction
By BioStar 1896 days agogithub.com - 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...Tadpole: an assembler, error-corrector, and read-extender
By BioStar 1896 days agojgi.doe.gov - Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is...QuorUM: An Error Corrector for Illumina Reads
By BioStar 1896 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...Musket - a multistage k-mer spectrum based corrector
By BioStar 1896 days agomusket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...
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