NDLI: Using populations of human and microbial genomes for organism detection in metagenomes.

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Using populations of human and microbial genomes for organism detection in metagenomes.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Ames, Sasha K. Gardner, Shea N. Marti, Jose Manuel Slezak, Tom R. Gokhale, Maya B. Allen, Jonathan E.
Description	Author Affiliation: Ames SK ( Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA); Gardner SN ( Global Security Computer Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA); Marti JM ( Instituto de Física Corpuscular, CSIC-UVEG, E-46980 Valencia, Spain.); Slezak TR ( Global Security Computer Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA); Gokhale MB ( Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA); Allen JE ( Global Security Computer Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA)
Abstract	Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.184879.114
Journal	Genome Research
Issue Number	7
Volume Number	25
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2015-07-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Genome, Microbial Metagenome Metagenomics Microbiota Computational Biology Databases, Nucleic Acid Roc Curve Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Multiple whole-genome alignments without a reference organism.

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.

The human genome browser at UCSC.

Computational identification of operons in microbial genomes.

Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

OrthoMCL: identification of ortholog groups for eukaryotic genomes.

A comparative map of the zebrafish genome.

Using populations of human and microbial genomes for organism detection in metagenomes.

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