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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (214 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (670 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (831 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 (883 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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BioGPS: Spotlight on the Gene Expression Atlas
By Jit 2274 days agohttp://biogps.org/ - BioGPS opened 2016 with a publication in Nucleic Acids Research, right after the New Year holiday. Throughout the year, new designs for the site were being created, reviewed, adjusted, reviewed, adjusted, and more review/adjustments in anticipation...FRODOCK 2.0: fast protein–protein docking server
By Neel 2275 days ago Comments (1)frodock.chaconlab.org - frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select...DNA Nucleotide Counter
By Neel 2280 days agowww.dnabaser.com - DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2288 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...Long read assembly workshop !
By Rahul Nayak 2288 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...ClipCrop: a tool for detecting structural variations with single-base resolution using...
By Rahul Nayak 2288 days agogithub.com - This is a tool for detecting structural variations using soft-clipping information From SAM files. https://github.com/shinout/clipcropVariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2288 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...nQuire: a statistical framework for ploidy estimation using next generation sequencing
By Jit 2288 days agogithub.com - nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where...GenomeThreader: Gene Prediction Software
By Neel 2289 days agogenomethreader.org - GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via...S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
By Abhimanyu Singh 2290 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...
