Protocol for De novo Genome Assembly using Illumina Reads
...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...ew/42542/trimmomatic-command Genome Assembly:The object of this p...1202 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis...-j 4 make insatall Take the sugarcane genome Saccharum spontaneum L as an example. The genome is 8-ploid with 32 chromosome...f1: Ks standard analysis procedure of the whole genome...1153 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, Go...1 (2012). GAGE: GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg, S. L. et al. Genome Res. 2...1045 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (...optional) Alignment-level QC (picard, SAMtools) Genome-wide and amplicon coverage QC...variant screenshots with annotation tracks (ASCIIGenome)...875 days ago
Useful Bioinformatics Analysis Tools !
...Compressor of collections of genome sequences. •  ...obust relative compression of genomes with random access, Bio...Compressor of collections of genomes given in Variant Call Format...isper Experimental mapper of whole genome sequencing data. &bull...861 days ago
List of comparative genomics resources !
...species. BGDB -- Bovine Genome Database Find information ab...Reconstruction Tool Based on Whole Genomes Construct phylogenetic tree...d to biometric comparisons of whole genomes Conduct comparative b...risons of Multiple Vertebrate Genomes Access to whole genome alig...675 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 f...9. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containin...l;bo S., 2010 A draft sequence of the Neandertal genome. Scien...675 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources f...9. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containin...l;bo S., 2010 A draft sequence of the Neandertal genome. Scien...575 days ago
Interesting Bioinformatics Resources !
1. a reproducible workflow. https://www.youtube.com/watch?v=s3JldKoA0zw This two minute video will chan...rticles/nbt.3780 12. Five selfish reasons to work reproducibly https://genomebiology...539 days ago
Chromosome breakpoint - a breakup to remember
Chromosome breakpoint refers to the physical location where a chromosome is broken and rearranged. Chromosome breakage can occur spontaneously or be in...423 days ago