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Tophat

transdecoder for translate your mRNA to protein

Trimmomatic is a java tool for cut and filter reads

Trinity RNA-seq is a de novo transcriptome assembly software that uses RNA-seq data to reconstruct transcript sequences and estimate expression levels. It allows for comprehensive analysis of gene expression and isoform diversity in non-model organisms without a reference genome. Who said this?

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.

Capt to merger transcripts

Capt to merger transcripts

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.

IGV, and free reads map visualization

Samtools

sratools for manage SRA Files

Atom install, packages install. Some awesome packages for atom