Update README.md

Author: baraaorabi

README.md

@@ -1,2 +1,105 @@
 # Freddie
-Co-chaining of local alignments of long reads on gene DAGs
+## Installation
+
+The simplest way to install the dependencies is using [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/):
+
+```bash
+git clone https://baraaorabi@bitbucket.org/baraaorabi/freddie.git
+cd freddie
+conda env create -f environment.yml
+conda activate freddie
+```
+
+
+
+## Running Freddie
+
+There are few scripts/stages in Freddie:
+
+- `py/freddie_align.py`: Align reads using `deSALT` mapper. (Optional since freddie accepts any SAM/BAM file for next stages)
+
+- `py/freddie_split.py`: Partitions the reads into independent sets that can be processed in parallel
+-  `py/freddie_segment.py`: Computes the canonical segmentation for each read set
+-  `py/freddie_cluster.py`: Clusters the reads using their canonical segmentation representation
+-  `py/freddie_isoforms.py`: Generates consensus isoforms of each cluster and outputs them in `GTF` format
+
+### Align
+
+```
+py/freddie_align.py --reads <FASTA/FASTQ> --genome <FASTA> --out-desalt-index <DIR> --output <SAM>
+```
+
+Align takes the following arguments:
+
+- `--reads/-r`: space separated list of FASTA/FASTQ files of the reads
+- `--genome/-g`: FASTA file of the genome. Only needed to deSALT index if `--desalt-index` is not provided.
+
+- `--out-desalt-index/-od`: Path to output directory to store deSALT index.  Only needed to deSALT index if `--desalt-index` is not provided.
+- `--desalt/-d`: Path to deSALT executable. Default: `deSALT`
+- `--desalt-index/-i`: Path to deSALT index if it exists.
+- `--temporary-prefix/-m`: Temporary prefix for deSALT alignment files. Default: `<--output>.temp`
+- `--sequencer/-s`: Sequencer option for deSALT: `null`, `ccs`, `clr`, `ont1d`, or `ont2d`. Default: `null`
+- `--output/-o`: Output SAM file 
+
+### Split (aka partition)
+
+```
+py/freddie_split.py --sam <SAM/BAM> --output <SPLIT.TSV>
+```
+
+Align takes the following arguments:
+
+- `--sam/-s`: `SAM/BAM` file of read alignments from deSALT or any other split/splice long-read mapper.
+- `--sam-format/-f`: `--sam` file format: `bam` or `sam`. Default: infers format from `--sam` file extension
+
+- ``--output/-o`: Output TSV file of split stage. Default: `freddie_split.tsv`
+
+### Segment
+
+```
+py/freddie_segment.py --split-tsv <SPLIT.TSV> --reads <FASTQ/FASTA> --output <SEGMENT.TSV>
+```
+
+Align takes the following arguments:
+
+- `--split-tsv/-s`: `SPLIT.TSV` output of the split stage
+- `--reads/-r`: Space separated list of FASTA/FASTQ files of the reads
+- `--threads/-t`: Number of threads. Default: 1
+- `--sigma/-sd`: Standard deviation parameter for the Gaussian filter. Default: 5.0
+- `--threshold-rate/-tp`: Coverage percentage threshold for segments. Default: 0.90
+- `--variance-factor/-vf`: Variance factor for heuristic of prefixing breakpoints. Any breakpoint with signal greater than `<-vf>` times the standard deviation plus the average of the signals will be prefixed. Default: 3.0
+- `--max-problem-size/-mps`: Maximum allowed problem size after which the problem will be broken down uniformly. Default: 50
+- `--min-read-support-outside`: Minimum contrasting coverage support required for a breakpoint. Default: 3
+- ``--output/-o`: Output TSV file of segment stage. Default: `freddie_segment.tsv`
+
+### Cluster
+
+```
+py/freddie_cluster.py --segment-tsv <SEGMENT.TSV> --output <CLUSTER.TSV>
+```
+
+Align takes the following arguments:
+
+- `--segment-tsv/-s`: `SEGMENT.TSV` output of the segment stage
+- `--gap-offset/-go`: Constant +/- slack used in unaligned gap condition. Default: 20
+- `--epsilon/-e`: +/- ratio of length as slack used in unaligned gap condition. Default: 0.2
+- `--max-rounds/-mr`: Maximum allowed number of rounds per sub-partition of a read set. Default: 30
+- `--min-isoform-size/-is`: Minimum read support allowed for an isoform. Default: 3
+- `--timeout/-to`: Gurobi timeout per isoform in minutes. Default: 4
+- `--threads/-t`: Number of threads. Default: 1
+- `--logs-dir/-l`: Directory path where logs will be outputted. Default: No logging
+- `--output/-o`: Output TSV file of cluster stage. Default: `freddie_cluster.tsv`
+
+### Isoforms
+
+```
+py/freddie_isoforms.py --segment-tsv <SEGMENT.TSV> --cluster-tsv <CLUSTER.TSV> --output <ISOFORMS.GTF>
+```
+
+Align takes the following arguments:
+
+- `--segment-tsv/-s`: `SEGMENT.TSV` output of the segment stage
+- `--cluster-tsv/-s`: `CLUSTER.TSV` output of the cluster stage
+- `--output/-o`: Output GTF file of isoforms stage. Default: `freddie_isoforms.gtf`
+
+