Commit f9af8df8 authored by peguerin's avatar peguerin
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Update README.md

parent 8b9f631a
......@@ -77,23 +77,23 @@ You're ready to run the analysis. Now follow the instructions at [Running the pi
- BASH scripts
* [filter_raw_data.sh](00-scripts/step1/filter_raw_data.sh) : Keep only the CO1 sequences with lat/lon information
* `get_geo_coordinates.sh` : Uses [http://www.geonames.org/] to find missing coordinates of individual sequences from their textual information of location.
* [get_geo_coordinates.sh](00-scripts/step1/get_geo_coordinates.sh) : Uses [http://www.geonames.org/] to find missing coordinates of individual sequences from their textual information of location.
- PYTHON scripts
* `lat_long_DMS_DD_converter.py` : Converts from DMS format to DD format the given coordinates.
* [lat_long_DMS_DD_converter.py](00-scripts/step1/lat_long_DMS_DD_converter.py) : Converts from DMS format to DD format the given coordinates.
## 3.2 `00-scripts/step2` : georeferenced sequences alignments by species
- BASH scripts
* `seq_alnt_filtered_data.sh` : aligns sequences from the same species with MUSCLE and creates coordinates file for each sequence.
* `cluster_freshwater_vs_marine.sh` : according to a list of marine species, moves the fasta and coords files into marine, freshwater repertories.
* [seq_alnt_filtered_data.sh](00-scripts/step2/seq_alnt_filtered_data.sh) : aligns sequences from the same species with MUSCLE and creates coordinates file for each sequence.
* [cluster_freshwater_vs_marine.sh](00-scripts/step2/cluster_freshwater_vs_marine.sh) : according to a list of marine species, moves the fasta and coords files into marine, freshwater repertories.
- PYTHON scripts
* `fasta_coords_files_species_generator.py` : extracts sequences and associated coordinates from the filtered data.
* [fasta_coords_files_species_generator.py](00-scripts/step2/fasta_coords_files_species_generator.py) : extracts sequences and associated coordinates from the filtered data.
- R scripts
* `equalareacoords.R` : attributes at each sequence an ID of cell of the shapefile of worldmap equal area projection from its coordinates.
* `equalarea_worldcoast.R` : relou
* [equalareacoords.R](00-scripts/step2/equalareacoords.R) : attributes at each sequence an ID of cell of the shapefile of worldmap equal area projection from its coordinates.
* [equalarea_worldcoast.R](00-scripts/step2/equalarea_worldcoast.R) : PAS ENCORE DECRIT !!!
## 3.3 `00-scripts/step3` : filter raw data
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