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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (216 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (673 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (834 days ago): Sequencing coverage is defined as the average number of reads that covers...
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BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and...
By Jit 3054 days agobioinf.uni-greifswald.de - Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction...Sushi: An R/Bioconductor package for visualizing genomic data
By Jit 3055 days agowww.bioconductor.org - Sushi: An R/Bioconductor package for visualizing genomic dataKa, Ks and Ka/Ks calculations
By Poonam Mahapatra 3056 days agolonglab.uchicago.edu - gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including...Useful Bioinformatics Tools
By Poonam Mahapatra 3057 days ago Comments (1)molbiol-tools.ca - Collections of few handy tools for bioinformatician http://molbiol-tools.ca/Convert.htmGene Finding and Predictions
By Poonam Mahapatra 3060 days agogenome.crg.es - In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by...GeneValidator - Identify problems with predicted genes
By Poonam Mahapatra 3060 days agogithub.com - GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene...LUMPY
By Shruti Paniwala 3061 days agogithub.com - A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...TGNet
By Shruti Paniwala 3062 days agogithub.com - Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of...GeneMANIA
By Jit 3063 days agohttp://genemania.org/ - Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function...vcfR
By Archana Malhotra 3067 days agocran.r-project.org - Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in...
