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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (623 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (784 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 (836 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Breeding Insight
By BioStar 1415 days agowww.breedinginsight.org - Breeding Insight at Cornell University will leverage recent improvements in genomics and open source informatics components, and in partnership with small breeding programs, will enable these programs to harness powerful digital...Breedbase is a comprehensive breeding management and analysis software
By BioStar 1415 days agohttps://breedbase.org/ - Breedbase is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high...Genomic Open-source Breeding informatics initiative
By BioStar 1415 days agocbsugobii05.biohpc.cornell.edu - To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs. To transform breeding by connecting diverse data with precision...bioinformatics workbook
By biogeek 1416 days agobioinformaticsworkbook.org - This books assumes that the reader has some knowledge of biology and basic understanding of the Unix command line. However, for the beginner, the appendix contains introductory material and tips/tricks for common bioinformatic problems, that is...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1420 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...Galaxy Training Resources !
By Jit 1426 days agotraining.galaxyproject.org - Welcome to Galaxy Training! Collection of tutorials developed and maintained by the worldwide Galaxy community TopicTutorials Introduction to Galaxy Analyses 10 Assembly 6 Climate 3 Computational...Genome assembly training tutorial at Galaxy !
By Jit 1426 days ago Comments (1)training.galaxyproject.org - In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull...EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
By Shruti Paniwala 1427 days agogithub.com - EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1427 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 1429 days agogithub.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...
