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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (201 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (657 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (818 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 (871 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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biostarhandbook
By Neel 1218 days agowww.biostarhandbook.com - Nice book collection for bioinformatician ... highly recommended.Applying MinHash to cluster RNAseq samples
By Neel 1218 days agoivory.idyll.org - A kmer blog worth spending time onk-mers tutorial - classification and taxonomy
By Neel 1218 days agoivory.idyll.org - DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently. More recently, we've...Genome Assembly Workshop 2020
By Jit 1219 days agoucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...RNA-Seq differential expression work flow using DESeq2
By BioStar 1221 days agowww.sthda.com - One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.The Snakemake Wrappers repository
By BioStar 1225 days agosnakemake-wrappers.readthedocs.io - The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows. More at https://github.com/snakemake/snakemake-wrappersUnderstanding kmer !
By BioStar 1226 days agobioinfologics.github.io - What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get...Kmer: a suite of tools for DNA sequence analysis
By BioStar 1227 days agohelp.rc.ufl.edu - More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome assemblies (same species), or between two different genomes (cross...JumboDB: tool for de Bruijn graph construction
By BioStar 1227 days agogithub.com - jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn...QuasR: Quantification and annotation of short reads in R
By Neel 1231 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...
