https://github.com/luizirber/leafnosed
https://github.com/luizirber/leafnosed
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/luizirber/leafnosed
- Owner: luizirber
- License: other
- Created: 2015-07-21T02:39:22.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2016-01-20T16:14:23.000Z (over 9 years ago)
- Last Synced: 2025-07-21T16:22:35.051Z (3 months ago)
- Language: Python
- Size: 3.45 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# California leaf-nosed bat (*Macrotus californicus*) genome assembly
# Getting started
## Dependencies
- FastQC (0.11.2 or greater)
- Snakemake (depends on Python 3)
- Make
## Configuration
There is a `conf.py` file containing constants and configuration.
Set it up accordingly for your system.
## Running
The Makefile contains the 'bootstrap' for Snakemake (download raw data and prepare
the raw data file list).
```bash
$ make
```
For subsequent runs and other steps you can invoke Snakemake directly:
```bash
$ snakemake
```
# Analysis steps
## Raw reads quality control
FastQC generates a report for both Illumina and PacBio raw reads.
The following rule executes FastQC with the appropriate files and publish the reports
to a remote SSH host.
```bash
$ snakemake publish_fastqc
```