Similar protocols

Pipeline publication

[…] ce to phylogenetic and population studies based on mtDNA data, which will be of use as we investigate the evolutionary history of this biodiversity hotspot., Raw shotgun data are deposited in the SRA under bioproject number PRJNA361218 and are available in the GigaScience repository, GigaDB []. Details of the method to support this work can be found in protocols.io []., 1. Additional file 1: DNA extraction of historical samples, library construction, and primer information, 2. Additional file 2: Sample information sheet of mitogenomes assembled in this work, 3. Additional file 3: Alignment of mitogenomes assembled in this work, 4. Additional file 4: Newick file for phylogenetic tree, BLAST: Basic Local Alignment Search Tool; bp: base pair; GATK: Genome Analysis Toolkit; MAFFT: Multiple Alignment using Fast Fourier Transform; NCBI RefSeq: National Center for Biotechnology Information Reference Sequence Database; PCR: polymerase chain reaction; RAxML: Randomized Axelerated Maximum Likelihood; SE: southeast., The authors declare that they have no competing interests., This project was funded by the Malaysian Government (F.M.S.), Lundbeck Foundation grant R52–5062 (M.T.P.G.), Leibniz-Association grant SAW-2013-IZW-2 (J.F.), the German Federal Ministry of Education and Research grant BMBF FKZ: 01LN1301A (A.W.), and the German Primate Center (C.R.)., F.M.S., A.W., J.F., and M.T.P.G. conceived the project. F.M.S., M.H.S.S., M.S.S., M.S.A., R.M., P.R.P., C.R., B.K.L., and S.J.R. collected the samples and extracted the genomic DNA. F.M.S., R.M., P.R.P., and C.R. constructed the libraries and did sequencing. F.M.S., J.R.M., F.P., S.L., P.R.P., R. […]

Pipeline specifications

Software tools BLASTN, GATK, MAFFT, RAxML
Databases GigaDB