# Pipelines

Pipelines in SAW generally assemble several programming modules which are designed to handle specific analysis tasks individually, for diverse requirements. 

## Main pipeline

[**SAW count**](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.2/analysis/pipelines/count) is the central component of the software suite, compatible with most Stereo-seq FF, Stereo-seq FFPE and Stereo-CITE FF datasets. The inputs consist of a chip mask, FASTQ files, a reference and a microscope image. So that the pipeline counts feature expression reads to generate expression matrices and analysis results from the Stereo-seq chip.

## Complementary pipelines

The complementary pipelines include:

* [`SAW makeRef`](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.2/tutorials/preparation-of-reference#saw-makeref): prepare for the reference index files. GTF/GFF and FASTA files or additional specific rRNA FASTA files are needed;
* [`SAW chechGTF`](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.2/tutorials/preparation-of-reference#saw-checkgtf): check whether an annotation file (GTF/GFF) is in the standard format, used in `SAW count`. In addition, extract specific information from GTF/GFF;
* [`SAW realign`](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.2/tutorials/with-manually-processed-files): accept the modified image `.tar.gz` from StereoMap, to generate the results of manual processes;
* [`SAW reanalyze`](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.2/tutorials/secondary-analysis): reanalyze the matrices to generate results, mainly including clustering analysis, lasso and differential expression analysis;
* [`SAW convert`](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.2/tutorials/format-conversion): provide tools for file format conversions;

of which the purpose is to support the main pipeline `SAW count` and ensure smooth, convenient processing of the entire analysis.