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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (637 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1094 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1254 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 (1307 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Cactus: a reference-free whole-genome multiple alignment program
By Jit 2399 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 2404 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 2405 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 2409 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 2417 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 2417 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 2417 days agogithub.com - This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 2433 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...GffCompare: Program for processing GTF/GFF files
By Jit 2433 days agoccb.jhu.edu - The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets
By Neel 2436 days agogithub.com - Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Developper: Gaëtan Benoit, PhD, former member of...
