Results for "human reference genome"
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Run bash script in Perl program !
BioPerl is a compilation of Perl modules that can be used to build bioinformatics-related Perl scripts. It is used, f...); HELP Here are some useful Perl cheat sheets that can be used as a quick refere...679 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analys...miniconda3/envs/wgd/make -j 4 make insatall Take the sugarcane genome Saccharum spontaneum L as an example. The genome is 8-ploid with 32 chromosome...1197 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...012). GAGE: GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012). KMC:...1088 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files...lignment-level QC (picard, SAMtools) Genome-wide and amplicon coverage QC pl...eenshots with annotation tracks (ASCIIGenome) Intersect variants acro...es || Unicycler || minia) Blast to reference genome (blastn) Contiguat...918 days ago
Useful Bioinformatics Analysis Tools !
...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 genomes given in Variant Call Format...905 days ago
List of comparative genomics resources !
...nt cluster variations between human and mouse View AREs in the human transcriptome and study the c...es of gene and transcripts in human and mouse. DroSpeGe -- ra...risons of Multiple Vertebrate Genomes Access to whole genome alig...ase dedicated to the study of genome conservation. OMA -- the...719 days ago
Online resources on must-read papers in evolutionary biology, for a literature club
...09. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1...S., 2010 A draft sequence of the Neandertal genome. Science 328: 710-722. Qua...d Ryan, M.J. 1991. The evolution of mating preferences and the paradox of the le...718 days ago
Must read paper and books in evolution biology !
...09. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1...S., 2010 A draft sequence of the Neandertal genome. Science 328: 710-722. Qua...d Ryan, M.J. 1991. The evolution of mating preferences and the paradox of the le...619 days ago
Common methods to discover tandem repeats
Tandem repeats are DNA seq...peated in a contiguous manner in the genome. These sequences are often us...ds for discovering tandem repeats in genomes: Tandem Repeat Finder:...hensively identify tandem repeats in genomes....465 days ago
Common steps for reads mapping !
Mapping reads to a reference genome is an essential step in many typ...arch question. Index the reference genome: Before mapping reads, the re...es specifying the input data, reference genome, and output file format....465 days ago
