A New start

README.md

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+# SeqPanther
+
+SeqPanther tool consists set of commands as follows:
+
+*   **seqpatcher** : integrates sanger sequencing of missing regions of an incomplete assembly to the assembly. This command is modification of [SeqPatcher tool](https://github.com/krisp-kwazulu-natal/seqPatcher)
+
+*   **codoncounter** : performs variant calling, generates nucleotide stats at variant sites and reports impacts of nucleotide changes on amino acids in the translated proteins.
+
+*   **transform** : performs transformation of codoncounter output in a format where user can select variant to integrate in the reference or assemblies using **nucsub** command.
+
+*   **nucsub** : integrates the alteration list generated by codoncounter in a given reference or assembled genome based on the user recommendations. <!--Providing options to users to select changes of their interests-->
+
+## Operating system compatibility
+
+Unix platforms.
+
+## Dependencies
+
+The tool relies on multiple external programs and python modules as listed below:
+
+### External Tools
+
+1.  Muscle
+
+*   To perform multiple sequence alignment
+*   Can be downloaded and install from
+*   `conda install muscle` to install
+
+2.  BLAT
+
+*   To query sequence location in the genome.
+*   `conda install blat` to install
+
+## Python modules
+
+<!-- TODO: Versions need to be included -->
+
+All the python module used for this program is listed in `requirements.txt`.
+
+# Installation
+
+## Manual installation
+
+1.  `pip install -r requirements.txt`
+2.  `python setup.py install`
+
+## Directly from the repo
+
+`pip install git+https://github.com/codemeleon/seqPanther.git`
+
+# Usages
+
+The commands are selft explanatory.
+
+seqPanther contains three commands, which can be accessed using `seqPanther --help`
+
+## CodonCounter
+
+This command can be used as `seqPanther CodonCounter`. The help accessible at `seqPanther CodonCounter --help` or [CodonCounter GitHub page](https://github.com/codemeleon/CodonCounter)
+
+## SeqIn
+
+This command can be used as `seqPanther SeqIn`. The help accessible at `seqPanther SeqIn --help` or [SeqIn GitHub page](https://github.com/codemeleon/SeqIn)
+
+## SeqPatcher
+
+This command can be used as `seqPanther SeqPatcher`. The help accessible at `seqPanther SeqPatcher --help` or [SeqPatcher GitHub page](https://github.com/CERI-KRISP/SeqPatcher)
+
+# Features
+
+Codon Counter and SeqIn commands were specifically defined for this program. However, each sub-command can be installed and used independently of this program.
+
+# Bug reporting
+
+Please report bugs on this portal or associated GitHub repos of the command
+
+# Cite
+
+If you use this tool, please cite it as
+
+    Bib for the opensource software journal (JOSS)