Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly met...hod for small to medium-sized genomes. What is de novo genome assembly?The method of taking...the DNA originated relates to genome assembly. No previous knowled...on a sequencing computer in a genome sequencing experiment. Depend...1198 days ago
Run bash script in Perl program !
BioPerl is a compilation of Perl modules that can be used to build bioinformatics-relate...to determine which feature is unique to a situation. Perl provides various features and operators for the executi...631 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis, and the othe...envs/wgd/make -j 4 make insatall Take the sugarcane genome Saccharum spontaneum L as an example. The genome i...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, Goulder..., 10-1 (2012). GAGE: GAGE: A critical evaluation of genome asse...lies and assembly algorithms. Salzberg, S. L. et al. Genome R...1041 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp...ard; optional) Alignment-level QC (picard, SAMtools) Genome-wide...idual variant screenshots with annotation tracks (ASCIIGenome)...871 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagenomic sequencing experiment...p;CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE,...C Compressor of collections of genome sequences. •  ...;Robust relative compression of genomes wit...C Compressor of collections of genomes...857 days ago
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List of comparative genomics resources !
...- evolutionary visualizer for overlapping genes Analyze the evolutionary process of overlapping genes when comparing differen...ase dedicated to the study of genome conservation. OMA -- the Orth...ar genomes that show sequence features, base composition plots, anal...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...95-609. 1b. Sachidandam et al. 2001. A map of human genome sequ...;äbo S., 2010 A draft sequence of the Neandertal genome....671 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for...95-609. 1b. Sachidandam et al. 2001. A map of human genome sequ...;äbo S., 2010 A draft sequence of the Neandertal genome....571 days ago