Latest comments
Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (202 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (658 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (819 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 (871 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
Tag cloud
Bioinformatics, Genome, NGS, assembly, Analysis, tool, reads, Sequencing, Data, alignment, Sequence, Visualization, R, Pipeline, Computational Biology, Genomics, genomes, Annotation, Long, Tools, Tutorial, Software, Fast, Gene, DNA, Plot, sequences, Genomic, Assemblies, PacBio, Package, Assembler, de novo, Synteny, Learn, read, Chromosome, accurate, Interactive, Perl, nanopore, genes, Program, Web, Scaffolding, Database, Server, Python, Mapping, Comparative
Our Sponsors
All site bookmarks
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
By Neel 1492 days agohttp://www.ub.edu/dnasp/ - DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some...IRscope: an online program to visualize the junction sites of chloroplast genomes
By Neel 1492 days agosites.google.com - eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust...vsFilt: A tool to improve virtual screening by structural filtration of docking poses
By Neel 1493 days agobiokinet.belozersky.msu.ru - The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition,...Updated science-wide author databases of standardized citation indicators
By Jit 1502 days agojournals.plos.org - There was great interest in the databases of standardized citation metrics across all scientists and scientific disciplines [1], and many scientists urged us to provide updates of the databases. Accordingly, we have provided updated analyses that...CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
By Shruti Paniwala 1506 days agogitlab.gwdg.de - CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 1507 days agobenjjneb.github.io - The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample. The DADA2...FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ...
By Shruti Paniwala 1508 days agogithub.com - FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The...Platypus – R package for object detection and image segmentation.
By BioStar 1509 days agogithub.com - platypus is an R package for object detection and semantic segmentation. Currently using platypus you can perform: multi-class semantic segmentation using U-Net architecture multi-class object detection...URMAP, an ultra-fast read mapper
By Jit 1519 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1522 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....
