cleaned up and added readme file

README.md

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+# Tranquilizer
+
+Tranquilizer is a Deep Learning (DL) based tool to annotate, visualize the annotated reads, demultiplex for single-cell long-reads data including **TRAQNUIL-seq** and **scNanoRNASeq** and generate some inital QC plots. 
+
+## I/O
+
+The directory storing all the raw reads in **fasta/fa/fasta.gz/fa.gz/fastq/fq/fastq.gz/fq.gz** is provided as the input and the tool generates demultiplexed fasta files along with valid and invalid annotated **.parquet** files and some QC .pdf files as the outputs in two separate steps/commands (preprocessfasta and annotate-reads). Check out the examples drectory for both **TRAQNUIL-seq** and **scNanoRNASeq** datasets.
+
+## Usage
+
+### <ins>Preprocessing</ins>
+
+To enhance the efficiency of the annotation process, Tranquilizer organizes raw reads into separate .parquet files, grouping them based on their lengths. This approach optimizes data compression within each bin, accelerates the annotation of the entire dataset, and facilitates the visualization of user-specified annotated reads without dependence on the annotation status of the complete dataset.
+
+Example usage:
+
+```console
+tranquilizer preprocessfasta /path/to/RAW_DATA/directory /path/to/OUTPUT/directory CPU_THREADS
+```
+It is recommended that you follow the directory structure as in the exmples.
+
+### <ins>Read length distribution</ins>
+
+As an initial quality control metric, users may wish to visualize the read length distribution. The `readlengthdist` command facilitates this by generating a plot with log10-transformed read lengths on the x-axis and their corresponding frequencies on the y-axis. The output is provided in .png format in the **/path/to/OUTPUT/directory/plots/** folder.
+
+Example uage:
+
+```console
+tranquilizer readlengthdist /path/to/OUTPUT/directory
+```
+
+### <ins>Annotation, barcode correction and demultiplexing</ins>
+
+Reads can be annotated, followed by barcode extraction, correction, and assignment to their respective cells (demultiplexing), using the single command `annotate-reads`. This command produces the following outputs:
+* Demultiplexed FASTA files: Located in /path/to/OUTPUT/directory/demuxed_fasta/.
+* Annotation metadata:
+	1. Valid reads: /path/to/OUTPUT/directory/annotations_valid.parquet
+    2. Invalid reads: /path/to/OUTPUT/directory/annotations_invalid.parquet
+* Quality control (QC) plots:
+    1. barcode_plots.pdf
+    2. demux_plots.pdf
+    3. full_read_annots.pdf
+All QC plots are saved in /path/to/OUTPUT/directory/plots/.
+
+**Note**: Before running the annotate-reads command, ensure you select the appropriate model for your dataset. If unsure, use the command `tranquilizer availablemodels` to view the available models.
+
+Example usage:
+
+```console
+tranquilizer annotate-reads MODEL_NAME /path/to/OUTPUT/directory /path/to/BARCODE_WHITELIST --chunk-size 100000 --portion full --njobs @CPU_threads
+```
+
+### <ins>Read visualization</ins>
+
+Annotated reads can be inspected independently of the `annotate-reads` process—either before or after successfully running the `annotate-reads` command—by providing their names to the `visualize` command. The resulting visualization is saved as a .pdf file in the **/path/to/OUTPUT/directory/plots/** folder.
+
+Example usage:
+
+```console
+tranquilizer visualize MODEL_NAME /path/to/OUTPUT/directory --portion full --read-names READ_NAME_1,READ_NAME_2,READ_NAME3
+``` 
+
+
+
+** Installation instructions and pre-requisites coming soon **