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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (209 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (666 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (827 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 (879 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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‘dockr’: the R container
By Jit 1838 days agowww.docker.com - dockr 0.8.6 is now available on CRAN. dockr is a minimal toolkit to build a lightweight Docker container image for your R package, in which the package itself is available. The Docker image seeks to mirror your R session as close as possible with...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 1840 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...HaploTypo: a variant-calling pipeline for phased genomes
By Jit 1842 days agogithub.com - An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve...SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
By Jit 1846 days agoacademic.oup.com - The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation...phyloXML: XML for evolutionary biology and comparative genomics
By Jit 1853 days agohttp://www.phyloxml.org/ - phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch...Minipolish: A tool for Racon polishing of miniasm assemblies
By BioStar 1859 days agogithub.com - Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long...RepeatModeler2: automated genomic discovery of transposable element families
By Neel 1860 days agogithub.com - RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open...simuG: a general-purpose genome simulator
By BioStar 1864 days agogithub.com - Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single...Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the...
By Rahul Nayak 1865 days agopypi.org - The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also...Seq: A high-performance, Pythonic language for bioinformatics
By Rahul Nayak 1868 days agohttps://seq-lang.org - Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing...
