Bioinformatics tools for telomere to telomere assembly !
● Merfin – k-mer-based assembly and variant callin... @rocioadh)● tama (Transcriptome Annotation by Modular Algorithms) &ndash...reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin @kr...1006 days ago
Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly met...nstitute.org/igv/ Automated and semi automated annotation tools:Prokka - https://github...http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/RapidAnnotationServerJCVI Annotation Service...1219 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis, and the other...with 32 chromosomes (2n = 4x8 = 32) Download the tutorial for CDS and GFF annotation files mkdir -p wgd_tutoria...1169 days ago
Frequently used bioinformatics tools for viral genome analysis !
IVA: accurate de novo assembly of RNA virus genomes. Hunt M, Gall A, Ong SH, Brener J, Ferns...puting, Vienna, Austria. URL http://www.R-project.org/. RATT: RATT: Rapid Annotation Transfer Tool. Otto, T. D., D...1061 days ago
Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake “...948 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC)...ools; default for metagenomics data) Variant annotation (SnpEff, SnpSift) Consensus...Nextclade) Individual variant screenshots with annotation tracks (ASCIIGenome) Int...891 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagenomic sequencing experiment...ultiple sequence alignments of proteins. • Deorowic...A., CoMSA: compression of protein multiple sequence alignment f...designed for huge families of proteins (even con...gh-quality alignments of large protein fa...877 days ago
List of comparative genomics resources !
3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes C...phylogenetics. PEDANT -- Protein Extraction, Description and ANal...-- a database of genome-wide annotations of regulatory sites Search...691 days ago
Online resources on must-read papers in evolutionary biology, for a literature club
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for exploring...79: 142-45. Testing for selection 1. McDonald & Kreitman. 1991. Adaptive protein ev...691 days ago
Understanding DUMP files from NCBI Taxonomy database !
*.dmp files are bcp-like dump from GenBank taxonomy database General information. Field terminator is "\t|\t" Row terminator is "\t|\n" nodes.dmp file consist...674 days ago