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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...
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Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial...
By Jit 1957 days agogithub.com - Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool...TRITEX sequence assembly pipeline for Triticeae genomes
By Jit 1963 days agotritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
By Jit 1971 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...Cactus: a reference-free whole-genome multiple alignment program
By Jit 1971 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...The Extensive de novo TE Annotator (EDTA)
By Abhimanyu Singh 1976 days agogithub.com - The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the...gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Jit 1977 days agogvolante.riken.jp - gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and...Artificial Intelligence Material !
By BioStar 1981 days agohttps://lnkd.in/f5aUbBM - Major Machine Learning Types Explianed in 11 Pages Credit: McKinsey For more applied resource you can see at: 1. Data Science Process https://lnkd.in/fMHtxYP 2. Data Visualization in Business https://lnkd.in/fYUCzgC 3. Understand How to answer...Patterns: a modeling tool dedicated to biological network modeling
By Abhimanyu Singh 1989 days ago Comments (1)github.com - It is designed to work with patterned data. Famous examples of problems related to patterned data are: recovering signals in networks after a stimulation (cascade network reverse engineering), analysing periodic signals.jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1989 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...Snakemake workflow: dna-seq-gatk-variant-calling
By Jit 1989 days agogithub.com - This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.
