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. Genome...1048 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (f...optional) Alignment-level QC (picard, SAMtools) Genome-wide and amplicon coverage QC...l variant screenshots with annotation tracks (ASCIIGenome)...878 days ago
Useful Bioinformatics Analysis Tools !
...obust relative compression of genomes with random access, Bio...Compressor of collections of genomes given in Variant Call Format...2: indel-sensitive short read mapping, bioRxiv.org, 2019;...sorting allows robust robust mapping of DNA sequencing data, ...865 days ago
List of comparative genomics resources !
...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 genome conservation. OMA -- the...organisms. UniGene Find mapping and expression information fo...678 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 fo...09. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containin...ml;bo S., 2010 A draft sequence of the Neandertal genome....678 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 consi...661 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources fo...09. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containin...ml;bo S., 2010 A draft sequence of the Neandertal genome....579 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 induced by e...426 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 genomes...424 days ago
Common steps for reads mapping !
Mapping reads to a reference genome is an essential step in many...e general steps to follow for mapping reads to a genome: Choose a read mapper: T...ion. Index the reference genome: Before mapping reads, the reference genome n...424 days ago