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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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Understanding HiFi Reads !
By Rahul Nayak 1007 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...Tiara: deep learning-based classification system for eukaryotic sequences
By Rahul Nayak 1017 days agoacademic.oup.com - With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of...kebabs: package provides functionality for kernel based analysis of biological sequences via...
By Rahul Nayak 1028 days agowww.bioinf.jku.at - The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define...SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
By Rahul Nayak 1031 days agotelatin.github.io - A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 1031 days agowww.genomicus.bio.ens.psl.eu - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...AGORA: Algorithm for Gene Order Reconstruction in Ancestors
By Jit 1031 days agogithub.com - AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was developed by Matthieu Muffato in the DYOGEN Laboratory at the École normale supérieure in Paris in 2008. // | | // ) ) // ) )...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1035 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...KAST
By Neel 1037 days agogithub.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.GToTree: a user-friendly workflow for phylogenomics
By Neel 1037 days agogithub.com - GToTree is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees. The open-access Bioinformatics Journal publication is available here, and documentation and examples can...AnchorWave
By Neel 1037 days agogithub.com - AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor...
