jhuanglab / iseq

An integrated analysis toolkit and pipeline for Next-Generation Sequencing (NGS) panel sequencing data

iseq

iseq is an integrated analysis toolkit and pipeline for NGS panel sequencing data. If you have any question about this tool, please contact us.

Python class of iseq: ReffaFile, FastqFile, BamFile, SamFile, VcfFile, CsvFile, MpileupFile and ResultFile.

Processor of iseq: preprocess, variantcaller, refinement

Pipeline: panel, panel_somatic

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

Install

source code

# Download the source code and gunzip
./install.R

Usage

configuration file is an important file to run iseq. Three type of parameters can be found in this file:

• tools
• extra files
• non-file type parameters

Tools: Command line tools, class of iseq can use these tools by self.cfg, e.g self.cfg["gatk"] (Need to download and install)

Extra files: Some of files required to run tools (Need to download)

Non-file type parameters: Other parameters (Do not need to download anything)

Germline Mode

# fastq2vcf mode
panel -c config.cfg \
         -s A01A \
         -m fastq2vcf \
         -1 A01A_1.fq.gz \
         -2 A01A_2.fq.gz \
         --bamprocess 00101111 \
         -o outdir

# fastq2bam
panel -c config.cfg \
         -s A01A \
         -m fastq2bam \
         -1 A01A_1.fq.gz \
         -2 A01A_2.fq.gz \
         --bamprocess 00101111 \
         -o outdir

# bam2vcf
panel -c config.cfg \
         -s A01A \
         -m bam2vcf \
         --in_bam A01A.bam \
         --bamprocess 00000000 \
         -o outdir

# genomeindex mode
panel -c config.cfg -m genomeindex

Somatic Mode

# fastq2vcf mode
panel_somatic -c config.cfg \
                 -s A01 \
                 -m fastq2vcf \
                 -1 A01A_1.fq.gz \
                 -2 A01A_2.fq.gz \
                 -3 A01C_1.fq.gz \
                 -4 A01C_2.fq.gz \
                 --bamprocess 00101111 \
                 -o outdir

# fastq2bam mode
panel_somatic -c config.cfg \
                 -s A01 \
                 -m fastq2bam \
                 -1 A01A_1.fq.gz \
                 -2 A01A_2.fq.gz \
                 -3 A01C_1.fq.gz \
                 -4 A01C_2.fq.gz \
                 --bamprocess 00101111 \
                 -o outdir

# bam2vcf mode
panel_somatic -c config.cfg \
                 -s A01 \
                 -m bam2vcf \
                 --case_in_bam A01A.bam \
                 --control_in_bam A01C.bam \
                 --bamprocess 00000000 \
                 -o outdir

# genomeindex mode
panel_somatic -c config.cfg -m genomeindex