Eukaryotic mRNA Analysis (Reference based and de novo options available)
This pipeline uses NGS RNA-Seq data as input and produces results from multiple downstream analyses including but not limited to: sequencing data quality assessment, de novo transcription site annotation, variable splicing analysis, differential expression analysis, function annotation and enrichment analysis.
Long non-coding RNA Analysis
Long non-coding RNAs (lncRNA) are non-coding transcripts with lengths longer than 200 nt and known to play roles in chromatin organization and regulation. High-throughput sequencing technologies and bioinformatic have empowered our understanding lncRNA sequences and positioning information to identify lncRNAs with crucial regulatory functions. This pipeline provides lncRNA analysis in addition to analyses mentioned in the Eukaryotic mRNA Analysis pipeline.
16S/18S/ITS amplicon sequencing
The Amplicon Sequencing microbial diversity analysis pipeline was developed based on years of experience in microbial diversity project analysis. The pipeline contains standardized basic analysis, which covers the mainstream analysis content of current microbial research and personalized analysis. The analysis report is rich and comprehensive, with the option to perform diverse personal analysis. Additionally, samples and groups can be modified on the fly for additional customization and control.
Shotgun Metagenomics Analysis
The Shotgun Metagenomic Analysis pipeline uses NGS data from mixed genomic materials extracted from environmental samples. Included analyses provide detailed information on species diversity and abundance, population structure, phylogenetic relationship, functional genes, and correlation networks with environmental factors.
NGS-WGS Variant Analysis
The NGS-WGS Variant Analysis is an integrated variant detection pipeline that performs data quality control, sequence alignment, annotation, and gene mutation analysis. The pipeline follows GATK best practices for SNP and InDel detection and uses Manta for structural variant calling.
Genome Wide Association Study (GWAS)
The GWAS pipeline is a downstream analysis that takes previously generated VCF files and corresponding phenotype data for a cohort of individuals as input. Using specific statistical methodologies, GWAS aims to uncover genome-wide nucleotide variations correlated with phenotypic differences. It plays a crucial role in exploring functional genes associated with complex human diseases and intricate traits in plants and animals.
Bulk Segregation Analysis (BSA)
BSA analysis involves pooling individuals with extreme phenotypic traits from a segregating population. By comparing differential loci between the pooled samples, this approach rapidly identifies closely linked molecular markers associated with target genes. Widely used in genetic mapping of plants and animals, it is a valuable tool for marker-assisted breeding.
Evolutionary Genetics Analysis
The Evolutionary Genetics Analysis workflow leverages BMKGENE's extensive experience in genetic evolution projects and includes phylogenetic tree construction, linkage disequilibrium analysis, genetic diversity assessment, selective sweep identification, kinship analysis, principal component analysis, and population structure characterization.
