seqSight Manual

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