---
title: "Bioinformatics"
lang: ko
url: https://www.gereallife.com/ko/services/resources-bioinformatics.html
canonical: https://www.gereallife.com/ko/services/resources-bioinformatics.html
entity: Shanghai Gereallife Biotech Co., Ltd
updated: 2026-11-02
---
## 01Toolchain Overview

 

Core toolchains across all domains, covering mainstream bioinformatics needs

### Genomics tools

BWA、GATK、Samtools、ANNOVAR

### Transcriptomics tools

STAR、featureCounts、DESeq2、Salmon

### Proteomics tools

DIA-NN、Spectronaut、MaxQuant、Philosopher

### Metabolomics tools

XCMS、MS-DIAL、MetaboAnalyst、MZmine

 
 
 

## 02Genomics Analysis Pipeline

 

Complete pipeline from raw data to variant annotation

### Data QC

FastQC + MultiQC summary reports; adapter and low-quality read trimming (Trimmomatic / fastp)

### Alignment

BWA-MEM alignment to reference genomes (hg38 / mm10); Samtools sort & index

### Variant Calling

GATK HaplotypeCaller (germline) / Mutect2 (somatic)

### Variant Filtering

GATK VQSR / hard filtering to remove low-quality variants

### Variant Annotation

ANNOVAR / VEP / SnpEff annotation of variant function, frequency and pathogenicity

### Summary

VCF files, annotation tables, Circos plots, mutational-signature analysis

 
 
 

## 03Transcriptomics Analysis Pipeline

 

From RNA-seq data to differential-expression visualization

### Data QC

FastQC + MultiQC; Trimmomatic adapter trimming

### Alignment

STAR (recommended) / HISAT2 alignment to reference genomes

### Quantification

featureCounts / StringTie gene-count matrices

### Differential Expression

DESeq2 / edgeR differential-expression analysis, |log2FC| > 1, FDR < 0.05

### Functional Enrichment

clusterProfiler GO/KEGG enrichment; genome-wide GSEA

### Visualization

volcano plots, heatmaps, PCA plots, MA plots

 
 
 

## 04Proteomics Analysis Pipeline

 

From raw MS data to protein-interaction networks

### Raw MS Data

Thermo RAW / Bruker .d / WIFF raw files

### Database Search

DIA-NN library search / Spectronaut direct-DIA analysis, FDR < 1%

### Protein Quantification

MaxLFQ or Top3 quantification with log2 transformation

### Differential-Protein Screening

limma / MSstats，|log2FC| > 0.58, adjusted p < 0.05

### Functional Annotation

GO, KEGG, Reactome enrichment; protein-interaction networks (STRING)

### Visualization

volcano plots, heatmaps, PCA, PPI network diagrams

 
 
 

## 05Metabolomics Analysis Pipeline

 

From peak detection to metabolic-pathway visualization

### Peak Detection & Alignment

XCMS / MS-DIAL peak detection and retention-time alignment

### Metabolite Identification

MS1 m/z + MS/MS spectral matching (HMDB/METLIN/MassBank)

### Preprocessing

missing-value imputation (KNN), PQN normalization, log2 transformation

### Differential-Metabolite Screening

t-test + VIP（PLS-DA），VIP > 1, p < 0.05

### Pathway Analysis

MetaboAnalyst / KEGG pathway enrichment and topology analysis

### Visualization

volcano plots, box plots, heatmaps, pathway bubble charts

 
 
 

## 06Integration Tools

 

Tool selection for multi-omics data integration and visualization

 

| Tool / package | Use case | Input data type | Output |
| --- | --- | --- | --- |
| mixOmics (R) | Multi-Omics Integration | gene-expression, protein, metabolite matrices | DIABLO models, loading plots |
| MOFA (R/Python) | unsupervised multi-omics reduction | any multi-omics matrices | factor matrices, variance decomposition |
| WGCNA (R) | weighted gene co-expression networks | gene-expression matrices | module detection, module–trait association |
| Cytoscape + stringApp | network visualization & integration | protein/gene lists | interaction networks, enriched modules |
| iPath / Pathview (R) | pathway visualization | metabolite/gene lists | colored pathway maps |

 
 
 
 

## 07Analysis-Report Deliverables

 

Complete data-analysis deliverables meeting publication requirements

### Raw Data

raw files in FASTQ, RAW and WIFF formats with MD5 checksums

### Analysis Report

complete PDF analysis report with methods and result interpretation

### Charts & Tables

publication-grade vector graphics (AI/SVG/PDF) and editable Excel tables

### Cloud Platform

OmicsHub interactive analysis reports with online filtering and data download

 
 
 

## Q&AFAQ

 Should variant calling use HaplotypeCaller or Mutect2? GATK HaplotypeCaller is used for germline variants and Mutect2 for somatic variants, followed by GATK VQSR or hard filtering to remove low-quality variants. 
 STAR or HISAT2 for RNA-seq alignment, and what do I quantify with? The pipeline recommends STAR, or HISAT2, for alignment to reference genomes; featureCounts or StringTie then produce gene-count matrices. 
 What happens to my raw MS data before screening for differential proteins? Thermo RAW / Bruker .d / WIFF files go through a DIA-NN library search or Spectronaut direct-DIA analysis at FDR < 1%, then MaxLFQ or Top3 quantification with log2 transformation; limma or MSstats screens differential proteins. 
 How are differential metabolites selected? By t-test plus VIP from PLS-DA, using VIP > 1 and p < 0. 05; 
 Which files do I receive when the analysis is finished? Raw files in FASTQ, RAW and WIFF formats with MD5 checksums, a complete PDF analysis report, publication-grade vector graphics (AI/SVG/PDF), editable Excel tables and OmicsHub interactive analysis reports. 
 
 
 
 
 
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