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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (168 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (624 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (785 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 (838 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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ALE: Assembly Likelihood Estimator
By BioStar 627 days agogithub.com - Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.Circos visualization !
By BioStar 628 days agowlcb.oit.uci.edu - Circos visualization https://wlcb.oit.uci.edu/modules/index.htmlHeatmap Draw !
By BioStar 628 days agosoftware.broadinstitute.org - Server for heatmap generation ! https://software.broadinstitute.org/morpheus/Bioinformatics Training Collections !
By BioStar 629 days agogithub.com - Useful list of bioinformatics training collections @ https://github.com/sib-swiss/training-collectionUnderstanding GO analysis
By Neel 654 days agoadvaitabio.com - The confusion about gene ontology and gene ontology analysis can start right from the term itself. There are actually two different entities that are commonly referred to as gene ontology or “GO”: the ontology itself, which is a...Collection of Graph Visualization tools !
By Neel 668 days agopangenome.github.io - Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation...Python Mini Projects !
By BioStar 678 days agogithub.com - There is a directory for each chapter of the book. Each directory contains a test.py program you can use with pytest to check that you have written the program correctly. I have included a short README to describe each exercise....MPXV Bookmarks
By BioStar 706 days agowww.cdc.gov - MPVX infection across the globe https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.htmlHairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 718 days agohal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no...
