Processing Your SNP file with Python:

abi

Samtools

fastp is a fast and efficient tool for quality control and preprocessing of high-throughput sequencing data. It can perform adapter trimming, quality filtering, and read correction in a single pass, and supports various sequencing platforms and data formats.

FastQC is a quality control tool used to analyze high-throughput sequencing data. It provides detailed graphs and reports that help assess the quality of the data before further downstream analysis.

transdecoder for translate your mRNA to protein

IGV, and free reads map visualization

An standard pipeline for miRNA-Seq data processing.

An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

Tophat

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Trimmomatic is a java tool for cut and filter reads

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WGCNA introduction and Q&S

Capt to merger transcripts