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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (200 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (657 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (818 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 (870 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
By Shruti Paniwala 945 days agogitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...Quip: Aggressive compression of FASTQ, SAM and BAM files.
By Neel 947 days agogithub.com - This will help us to reduce the amount of drive space we take up and decrease data transfer times Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 952 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...Snakemake Tutorials !
By Rahul Nayak 962 days agocarpentries-incubator.github.io - A lesson introducing the Snakemake workflow system for bioinformatics analysis. Prerequisites This is an intermediate lesson and assumes learners have already done some bioinformatics: Familiarity with the BASH command shell, including...MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer...
By Rahul Nayak 974 days agogithub.com - MUM&Co is able to detect:Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)Inversions (>=1kb) and translocations (>=10kb)PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
By Rahul Nayak 980 days agogithub.com - PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 997 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...R Shiny in Life Sciences – Top 7 Dashboard Examples
By Neel 999 days agowww.r-bloggers.com - R Shiny is one of the easiest ways for developers to make production-ready dashboards when speed and functionality are crucial. Shiny is approachable with a lot of documentation available, and because of this, a lot of developers/researchers...The complete sequence of a human genome
By Neel 1000 days agowww.science.org - The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.Ten quick tips for deep learning in biology
By Neel 1006 days agojournals.plos.org - By taking a comprehensive and careful approach to deep learning based on critical thinking about research questions, planning to maintain rigor, and discerning how work might have far-reaching consequences with ethical dimensions, the life science...
