Gfkb - Revision history

Jkeeney at 14:18, 29 August 2025

2025-08-29T14:18:36Z

← Older revision		Revision as of 14:18, 29 August 2025
Line 7:		Line 7:

	We use a two-step pipeline for metagenomic analysis; CensuScope and Hexagon. CensuScope is a census-based tool that randomly samples a user-defined number of reads and BLASTs them against a reference DB. Our reference database (a filtered version of NTdb) is the NCBI Nucleotide db with all of the sequences lacking a clear taxonomic lineage filtered out. All artificial sequences have been removed either by our automated filter or manually, once an artificial sequence is identified during post analysis processing Sequences identified by CensuScope are used as references in Hexagon alignments. HIVE-hexagon, a K-mer based aligner, is more sensitive and faster than current standard alignment algorithms. HIVE-hexagon offers a decrease in computational cost, memory requirement and time for processing.		We use a two-step pipeline for metagenomic analysis; CensuScope and Hexagon. CensuScope is a census-based tool that randomly samples a user-defined number of reads and BLASTs them against a reference DB. Our reference database (a filtered version of NTdb) is the NCBI Nucleotide db with all of the sequences lacking a clear taxonomic lineage filtered out. All artificial sequences have been removed either by our automated filter or manually, once an artificial sequence is identified during post analysis processing Sequences identified by CensuScope are used as references in Hexagon alignments. HIVE-hexagon, a K-mer based aligner, is more sensitive and faster than current standard alignment algorithms. HIVE-hexagon offers a decrease in computational cost, memory requirement and time for processing.
			<br>
			<br>

	'''~~Publications~~'''		'''Current Slim NT database:'''

	~~<a target="_blank" href="~~https://~~doi~~.~~org~~/10.~~1186/1471-2164-15-918">Shamsaddini ''et al''~~.~~</a>~~		https://hive.biochemistry.gwu.edu/static/slimNT.fa.gz

	~~<a target="_blank" href="https~~:~~//doi.org/10.1371/journal.pone.0099033">Santana-Quintero '~~'~~et al~~''~~.</a>~~		'''Current Slim NT taxonomy database:'''

	~~<a target="_blank" href="~~https://~~doi~~.~~org/10~~.~~1093~~/~~database~~/~~baw022">Simonyan ''et al''~~.</a>		https://hive.biochemistry.gwu.edu/static/slimNT.db.gz
			<br>
	<~~a target="_blank" href="https://doi.org/10.3390/genes5040957">Simonyan V, Mazumder R</a~~>		<br>
			'''Publications'''
	~~Current Slim NT database:~~

	https://~~hive~~.~~biochemistry.gwu~~.~~edu/static~~/~~slimNT.fa~~.gz		[https://doi.org/10.1186/1471-2164-15-918 Shamsaddini ''et al''.]

	~~Current Slim NT taxonomy database~~:		[https://doi.org/10.1371/journal.pone.0099033 Santana-Quintero ''et al''.]

	https://~~hive~~.~~biochemistry~~.~~gwu.edu~~/~~static~~/~~slimNT.db~~.gz		[https://doi.org/10.1093/database/baw022 Simonyan ''et al''.]

			[https://doi.org/10.3390/genes5040957 Simonyan V, Mazumder R]
			<br>
			<br>
	'''Funding'''		'''Funding'''

	LOI_ID#L02496974, NSF_Lineage_Award #1546491		LOI_ID#L02496974, NSF_Lineage_Award #1546491
	</td></tr></table>		</td></tr></table>

Jkeeney: Added links to current SlimNT files.

2025-08-29T14:06:31Z

Added links to current SlimNT files.

← Older revision		Revision as of 14:06, 29 August 2025
Line 1:		Line 1:
	<table width=1100><tr><td>		<table width=1100><tr><td>
	~~<br>~~		<h5>Gutfeeling KnowledgeBase</h5><span style="font-size:13px;"> We have developed a proof-of-concept gut microbiome monitoring system prototype using a sequencing and analysis pipeline implemented during our previous I-Corps award (see below).</span>
	<h5>Gutfeeling KnowledgeBase</h5>
	~~<br>~~
	<span style="font-size:13px;">
	We have developed a proof-of-concept gut microbiome monitoring system prototype using a sequencing and analysis pipeline implemented during our previous I-Corps award (see below).
	<~~br><br~~>
	We have collected from the individuals enrolled in our study the following: three separate fecal samples for metagenomic sequencing, anthropometric measurements, a diet history questionnaire, gastrointestinal symptoms questionnaires, perceived stress questionnaires, physical activity questionnaires, and sleep questionnaires. We have also begun the analysis of fecal samples from the Human Microbiome Project and the associated metadata. The integration of this data into a single knowledgebase of comparable samples using our optimized pipeline will provide the real value of our prototype.

	<~~br><br><br~~>~~<br>~~		<span style="font-size:13px;"> We have collected from the individuals enrolled in our study the following: three separate fecal samples for metagenomic sequencing, anthropometric measurements, a diet history questionnaire, gastrointestinal symptoms questionnaires, perceived stress questionnaires, physical activity questionnaires, and sleep questionnaires. We have also begun the analysis of fecal samples from the Human Microbiome Project and the associated metadata. The integration of this data into a single knowledgebase of comparable samples using our optimized pipeline will provide the real value of our prototype.</span>
	~~<b>HIVE Metagenomics Pipeline</b>~~
	~~<br>~~
	We ~~use a two-step pipeline~~ for metagenomic ~~analysis; CensuScope~~ and ~~Hexagon~~. ~~CensuScope is a census-based tool that randomly~~ samples ~~a user-defined number of reads~~ and ~~BLASTs them against a reference DB~~.
	~~Our reference database (~~a ~~filtered version~~ of ~~NTdb) is~~ the ~~NCBI Nucleotide db with all~~ of ~~the sequences lacking a clear taxonomic lineage filtered out. All artificial sequences have been removed either by~~ our ~~automated filter or manually, once an artificial sequence is identified during post analysis processing~~
	Sequences identified by CensuScope are used as references in Hexagon alignments. HIVE-hexagon, a K-mer based aligner, is more sensitive and faster than current standard alignment algorithms. HIVE-hexagon offers a decrease in computational cost, memory requirement and time for processing.

			'''HIVE Metagenomics Pipeline'''

			We use a two-step pipeline for metagenomic analysis; CensuScope and Hexagon. CensuScope is a census-based tool that randomly samples a user-defined number of reads and BLASTs them against a reference DB. Our reference database (a filtered version of NTdb) is the NCBI Nucleotide db with all of the sequences lacking a clear taxonomic lineage filtered out. All artificial sequences have been removed either by our automated filter or manually, once an artificial sequence is identified during post analysis processing Sequences identified by CensuScope are used as references in Hexagon alignments. HIVE-hexagon, a K-mer based aligner, is more sensitive and faster than current standard alignment algorithms. HIVE-hexagon offers a decrease in computational cost, memory requirement and time for processing.

			'''Publications'''

			<a target="_blank" href="https://doi.org/10.1186/1471-2164-15-918">Shamsaddini ''et al''.</a>

			<a target="_blank" href="https://doi.org/10.1371/journal.pone.0099033">Santana-Quintero ''et al''.</a>

			<a target="_blank" href="https://doi.org/10.1093/database/baw022">Simonyan ''et al''.</a>

	~~<br><br><br><br>~~
	~~<b>Publications</b>~~
	~~<br>~~
	~~<a target="_blank" href="https://doi.org/10.1186/1471-2164-15-918">Shamsaddini <i>et al</i>.</a>~~
	~~<br><br>~~
	~~<a target="_blank" href="https://doi.org/10.1371/journal.pone.0099033">Santana-Quintero <i>et al</i>.</a>~~
	~~<br><br>~~
	~~<a target="_blank" href="https://doi.org/10.1093/database/baw022">Simonyan <i>et al</i>.</a>~~
	~~<br><br>~~
	<a target="_blank" href="https://doi.org/10.3390/genes5040957">Simonyan V, Mazumder R</a>		<a target="_blank" href="https://doi.org/10.3390/genes5040957">Simonyan V, Mazumder R</a>
	~~<br><br>~~

	~~<br><br><br><br>~~		Current Slim NT database:
	~~<b>Funding<~~/b>
	~~<br>~~		https://hive.biochemistry.gwu.edu/static/slimNT.fa.gz
	~~LOI_ID#L02496974, NSF_Lineage_Award #1546491~~
			Current Slim NT taxonomy database:

	</~~span>~~		https://hive.biochemistry.gwu.edu/static/slimNT.db.gz

			'''Funding'''

			LOI_ID#L02496974, NSF_Lineage_Award #1546491
	</td></tr></table>		</td></tr></table>

Jkeeney: Created page with "

Gutfeeling KnowledgeBase

We have developed a proof-of-concept gut microbiome monitoring system prototype using a sequencing and analysis pipeline implemented during our previous I-Corps award (see below).

We have collected from the individuals enrolled in our study the following: three separate fecal samples for metagenomic sequencing, anthropometric measurements, a diet history questio..."
2025-08-27T18:26:48Z

Created page with "<table width=1100><tr><td> <h5>Gutfeeling KnowledgeBase</h5> We have developed a proof-of-concept gut microbiome monitoring system prototype using a sequencing and analysis pipeline implemented during our previous I-Corps award (see below). We have collected from the individuals enrolled in our study the following: three separate fecal samples for metagenomic sequencing, anthropometric measurements, a diet history questio..."

New page
<table width=1100><tr><td>
 
<h5>Gutfeeling KnowledgeBase</h5>
 

We have developed a proof-of-concept gut microbiome monitoring system prototype using a sequencing and analysis pipeline implemented during our previous I-Corps award (see below).
 
We have collected from the individuals enrolled in our study the following: three separate fecal samples for metagenomic sequencing, anthropometric measurements, a diet history questionnaire, gastrointestinal symptoms questionnaires, perceived stress questionnaires, physical activity questionnaires, and sleep questionnaires. We have also begun the analysis of fecal samples from the Human Microbiome Project and the associated metadata. The integration of this data into a single knowledgebase of comparable samples using our optimized pipeline will provide the real value of our prototype.

 
HIVE Metagenomics Pipeline
 
We use a two-step pipeline for metagenomic analysis; CensuScope and Hexagon. CensuScope is a census-based tool that randomly samples a user-defined number of reads and BLASTs them against a reference DB.
Our reference database (a filtered version of NTdb) is the NCBI Nucleotide db with all of the sequences lacking a clear taxonomic lineage filtered out. All artificial sequences have been removed either by our automated filter or manually, once an artificial sequence is identified during post analysis processing
Sequences identified by CensuScope are used as references in Hexagon alignments. HIVE-hexagon, a K-mer based aligner, is more sensitive and faster than current standard alignment algorithms. HIVE-hexagon offers a decrease in computational cost, memory requirement and time for processing.

 
Publications
 
<a target="_blank" href="https://doi.org/10.1186/1471-2164-15-918">Shamsaddini et al.</a>
 
<a target="_blank" href="https://doi.org/10.1371/journal.pone.0099033">Santana-Quintero et al.</a>
 
<a target="_blank" href="https://doi.org/10.1093/database/baw022">Simonyan et al.</a>
 
<a target="_blank" href="https://doi.org/10.3390/genes5040957">Simonyan V, Mazumder R</a>
 

 
Funding
 
LOI_ID#L02496974, NSF_Lineage_Award #1546491



</td></tr></table>