From raw reads to trees : Whole genome SNP phylogenetics across

نویسندگان

  • Sanaa A. Ahmed
  • Chien-Chi Lo
  • Po-E Li
  • Karen W. Davenport
چکیده

1 From raw reads to trees: Whole genome SNP phylogenetics across the tree of 1 life 2 3 Sanaa A. Ahmed, Chien-Chi Lo, Po-E Li, Karen W. Davenport, and Patrick S. G. Chain 4 5 Biome Sciences, Bioscience Division, Los Alamos National Laboratory, MS-M888, Los 6 Alamos, NM 87545 7 Corresponding author: 8 Patrick S.G. Chain 9 Scientist IV 10 Los Alamos National Laboratory 11 MS-M888 12 Los Alamos, NM 87545 13 Email: [email protected] 14 Tel: 505-665-4019 15 Cell: 505-500-6072 16

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

From raw reads to trees : Whole genome SNP phylogenetics across the tree of 1 life 2 3

1 From raw reads to trees: Whole genome SNP phylogenetics across the tree of 1 life 2 3 Sanaa A. Ahmed, Chien-Chi Lo, Po-E Li, Karen W. Davenport, and Patrick S. G. Chain 4 5 Biome Sciences, Bioscience Division, Los Alamos National Laboratory, MS-M888, Los 6 Alamos, NM 87545 7 Corresponding author: 8 Patrick S.G. Chain 9 Scientist IV 10 Los Alamos National Laboratory 11 MS-M888 12 Los Alamos, N...

متن کامل

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

Effective use of rapid and inexpensive whole genome sequencing for microbes requires fast, memory efficient bioinformatics tools for sequence comparison. The kSNP v2 software finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation; better scaling for draft genomes available as assembled contigs or raw, unass...

متن کامل

Op-molb140061 1077..1088

Studies of microbial evolutionary dynamics are being transformed by the availability of affordable high-throughput sequencing technologies, which allow whole-genome sequencing of hundreds of related taxa in a single study. Reconstructing a phylogenetic tree of these taxa is generally a crucial step in any evolutionary analysis. Instead of constructing genome assemblies for all taxa, annotating ...

متن کامل

Identifying SNPs without a Reference Genome by Comparing Raw Reads

Next generation sequencing (NGS) technologies are being applied to many fields of biology, notably to survey the polymorphism across individuals of a species. However, while single nucleotide polymorphisms (SNPs) are almost routinely identified in model organisms, the detection of SNPs in non model species remains very challenging due to the fact that almost all methods rely on the use of a ref...

متن کامل

SNP-Seek database of SNPs derived from 3000 rice genomes

We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for conveni...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2015