Software in Bioinformatics
===============================

:Authors: Hailing Fang
:Created: 20260412
:Updated: 20260412



QC for Dequencing Data
----------------------------

- FastQC

- cutadapt

- Trimmomatic

- fastp


Read Aligner
--------------------------

- BWA

- bowtie2

- Hisat2

- STAR

- Minimap2

- Salmon

- kallisto


Sam File manipulation
------------------------

- Samtools

- bcftools



scRNA-seq Clustering
--------------------------

- Seurat

- Scanpy

- Monocle

- SingleR

- Harmony

- scvi-tools

- CellBender