Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes. What is de novo genome assembly?The method of taking a large num...1248 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis, and the other is based on the Ks distribution map. Among them, Ks is defined as the average...1199 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 P, Nastouli E, Keane JA, Kellam P, Otto TD. Bioinformatics. 2015 J...1091 days ago
Illumina based assembly pipeline steps !
...AMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (picard; optional) Alignment-level QC (picard, SAMtools) Genome-wide and amplicon coverage QC plot...921 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagenomic sequencing experiments. • Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-m...907 days ago
List of comparative genomics resources !
...ription and ANalysis Tool Conduct genome wide functional and structural analysis. PReMod -- a database of genome-wide mammalian cis-regulatory module predictions Conduct genome-wide cis-regulatory module (CRM) p...721 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 the literature: Barton, N. H., Briggs, D. E. G., Eisen, J. A., Go...721 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J. A., Go...621 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 used as genetic markers and are imp...467 days ago
Common steps for reads mapping !
Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here...467 days ago