Results for "genome notes"
Blogs
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis, and the other is based o.../miniconda3/envs/wgd/make -j 4 make insatall Take the sugarcane genome Saccharum spontaneum L as an example. The genom...1149 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 B, Gou...-1 (2012). GAGE: GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg, S. L. et al. Genom...1041 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fa...; optional) Alignment-level QC (picard, SAMtools) Genome-wide and amplicon coverage QC...al variant screenshots with annotation tracks (ASCIIGenom...871 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagenomic sequencing experime...CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE,...Compressor of collections of genome sequences. • ...obust relative compression of genomes with random access, Bio...Compressor of collections of genom...857 days ago
List of comparative genomics resources !
3D-GENOMICS -- A Database to Compare Structural and Functional A...species. BGDB -- Bovine Genome Database Find information ab...struction Tool Based on Whole Genomes Construct phylogenetic tree...risons of Multiple Vertebrate Genomes Access to whole genome alig...ase dedicated to the study of genom...671 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...609. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containin...uml;bo S., 2010 A draft sequence of the Neandertal genom...671 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for...609. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containin...uml;bo S., 2010 A draft sequence of the Neandertal genom...571 days ago
Common methods to discover tandem repeats
Tandem repeats are DNA sequences that are repeated in a contiguous manner in the genome. These sequences are often us...ods for discovering tandem repeats in genomes: Tandem Repeat Finder:...ehensively identify tandem repeats in genom...417 days ago
Common steps for reads mapping !
Mapping reads to a reference genome is an essential step in many types...ps to follow for mapping reads to a genome: Choose a read mapper: T...question. Index the reference genome: Before mapping reads, the re...pecifying the input data, reference genom...417 days ago
Steps to find palindrome in genomes !
Palindromes are sequences of nucleotides that...rward. They can be present in genomes and have various biological...or discovering palindromes in genomes: Direct sequence search...tify palindromic regions in a genome. It involves plotting the gen...By mapping these reads to the genom...417 days ago
