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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (636 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1092 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1253 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 (1305 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Genome Assembly Workshop 2020
By Jit 1654 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 1656 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 1660 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 1661 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 1661 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 1662 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 1666 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...Interactive Bioinformatics Resources !
By Jit 1667 days agohttp://sandbox.bio - Learn how to use bioinformatics tools right from your browser.Everything runs in a sandbox, so you can experiment all you want. More at sandbox.bioVentoy: an open source tool to create bootable USB drive
By LEGE 1711 days agogithub.com - Ventoy is an open source tool to create bootable USB drive for ISO/WIM/IMG/VHD(x)/EFI files. With ventoy, you don't need to format the disk over and over, you just need to copy the image files to the USB drive and boot it. You can copy many image...Calling variants in non-diploid systems
By Neel 1714 days ago Comments (1)training.galaxyproject.org - The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been...
