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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (310 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (767 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (928 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 (980 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1896 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...Nanopore adaptor !
By Jit 1898 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads....DMINDA2: an integrated web server for DNA motif identification and analyses
By BioStar 1898 days agobmbl.sdstate.edu - DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses More at http://bmbl.sdstate.edu/DMINDA2/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
By Jit 1898 days agogithub.com - identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina R. Arkhipova. "Massive horizontal gene transfer in...3D de novo assembly (3D DNA) pipeline
By Jit 1898 days agogithub.com - For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of the pipeline and to reproduce the...Nucleus: Python and C++ code for reading and writing genomics data.
By Jit 1899 days agogithub.com - Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework,...BioCoder : newsletter of that revolution. It’s about biology as it moves from research labs into...
By Jit 1899 days agowww.oreilly.com - BioCoder features: Novel therapeutic discovery strategies Hardware such as low-cost lab equipment or diagnostics Open or low-cost bioinformatics tools Engineered organisms for the production of small molecules, biologics, or other...AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome...
By Jit 1899 days agogithub.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1901 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...Google Colab : Google Colab is a free cloud service and now it supports free GPU!
By Jit 1901 days agocolab.research.google.com - You can: improve your Python programming language coding skills. develop deep learning applications using popular libraries such as Keras, TensorFlow, PyTorch, and OpenCV. If you have just a single notebook to submit, use the...
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