Introduction

iseq is a lightweight analysis pipeline for gene mutation analysis using NGS data, which can be used to execute several bioinfomatics softwares command in python and a integrity analysis work-flow for gene panel sequencing data.

Genome reference, Fastq, Sam, Bam, Vcf and other format files be packaged in divided module that you can implement some of foundamental or specific manipulation.

Mainly Feature:

• Multiple sequence alignment softwares
• Multiple variantion detection softwares
• Easy to use
• Extend easily
• Single configuration file do all things
• Output log be divided into in individual file

Requirements

• Java
• R
• BioInstaller
• GATK
• tvc
• bwa
• lofreq
• varscan2
• samtools
• vcftools
• picard
• ANNOVAR

Work Flow

Gene panel sequencing work flow:

FASTQ and/or BAM can be as the input and several quality control tools, like FastqQC/PRINSEQ/GATK, be used to filter raw data and get the clean FASTQ and/or BAM file. The mainly analysis step as followed.

• Map to Reference (FASTQ)
• Mark Duplicates (BAM)
• Base Recalibration (BAM)
• Indel Realignment (BAM)
• Variants Calling (BAM)
• Variants Annotation (VCF/CSV)
• Variants Filtration (VCF/CSV/Result)
• Visuliztion (Result)