seqSight Manual

seqSight is a tool to jointly profile microbial strains, genes, and biosynthetic gene clusters from metagenomics data; it is designed to provide maximum utility to the user by incorporating a number of analysis modules for the quantification of not only bacterial strains but also gene families and biosynthetic gene clusters. seqSight also incorporates quality control modules and visualization tools.

Module Introduction

Module Name	Description
lib	Database preparation: Generate a new database for any given taxa id or user could generate by themselves
map	Alignment process: Align the reads to the host/target genome database using the bowtie2 tool
id	Reassignment step: Apply the Bayesian reassignment model to handle the ambiguous reads
report	Report step: Compute the best hit result and generate the report

Workflow

Input type: fastq file

Output folder: relative _abundance.tsv

Function - [seqSight]

Name in short	Full Name	Data Structure	Default value	Description
-U		String	“path_of_input”	fastq, Single sequence
-1	- - input1	String	“path_of_input”	fastq, Pair-end sequence
-2	- - input2	String	“path_of_input”	fastq, Pair-end sequence
-outDir		String	“path_of_input”	Path of output folder
-targetIndexPrefixes		List(Comma Separated)	[“path_of_refdb”, “path_of_refdb”, …]	Reference database in bowtie2 format
-outName

Command

Case1 - unique input and bowtie2 reference database

seqSight -U seqSight/Test/TestData/ex1.fastq -outAlign seqSight/Test/TestData/outAlign.sam -targetIndexPrefixes seqSight/Test/TestData/genomes

Case2 - pair-end input and bowtie2 reference database

seqSight -1 seqSight/Test/TestData/PSM7J1BH_R1.fastq -2 seqSight/Test/TestData/PSM7J1BH_R2.fastq -outAlign seqSight/Test/TestData/outAlignPAIR.sam -targetIndexPrefixes seqSight/Test/TestData/genomes

Case3 - unique input and 2+ more fna reference database

seqSight -U seqSight/Test/TestData/ex1.fastq -outAlign seqSight/Test/TestData/outAlignBacUNIQUE.sam -targetRefFiles seqSight/Test/TestData/seqtk/bacteria.fna,seqSight/Test/TestData/genomes.fa

Function - [seqSight combineOutput]

Function - [seqSight barplot]

Methodology

Rescaling factor