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Commit b6b40156 authored by Smit, Sandra's avatar Smit, Sandra
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Updated README

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...@@ -134,13 +134,13 @@ Add the path to the java archive of PanTools, located in the /dist subdirectory ...@@ -134,13 +134,13 @@ Add the path to the java archive of PanTools, located in the /dist subdirectory
3 : high 3 : high
- *--out-format* or *-of* : Writes the alignment files in BAM|SAM|NONE format. - *--out-format* or *-of* : Writes the alignment files in BAM|SAM|NONE format.
- *--alignment-mode* or *-am* (**default value**: 2) : The alignment mode. - *--alignment-mode* or *-am* (**default value**: 2) : The alignment mode.
`-1 : Competitive, none-bests` ```-1 : Competitive, none-bests```
`-2 : Competitive, random-best` ```-2 : Competitive, random-best```
`-3 : Competitive, all-bests` ```-3 : Competitive, all-bests```
`1 : Normal, none-bests` ```1 : Normal, none-bests```
`2 : Normal, random-best` ```2 : Normal, random-best```
`3 : Normal, all-bests` ```3 : Normal, all-bests```
`0 : Normal, all-hits` ```0 : Normal, all-hits```
- *--interleaved* or *-i* : Process the fastq file as an interleaved paired-end archive. - *--interleaved* or *-i* : Process the fastq file as an interleaved paired-end archive.
...@@ -153,14 +153,8 @@ Add the path to the java archive of PanTools, located in the /dist subdirectory ...@@ -153,14 +153,8 @@ Add the path to the java archive of PanTools, located in the /dist subdirectory
The Neo4j browser allows you to visualize parts of the pangenome graph and run Cypher queries and receive the results in a tabular or a graphical format. You need to download the appropriate version of Neo4j (use the version subcommand to see the consistent version). To visualize a pangenome: The Neo4j browser allows you to visualize parts of the pangenome graph and run Cypher queries and receive the results in a tabular or a graphical format. You need to download the appropriate version of Neo4j (use the version subcommand to see the consistent version). To visualize a pangenome:
1. Add path to the Neo4j /bin directory to the path environment variable. 1. Add path to the Neo4j /bin directory to the path environment variable.
2. Add path to your pangenome in the Neo4j configuration file NEO4J-DIRECTORY/conf/neo4j.conf: 2. Add path to your pangenome in the Neo4j configuration file NEO4J-DIRECTORY/conf/neo4j.conf: ```dbms.directories.data = PATH_TO_THE_PANGENOME_DATABASE```
`dbms.directories.data = PATH_TO_THE_PANGENOME_DATABASE` 3. Start the Neo4j database server from the shell: `neo4j start`
3. Start the Neo4j database server from the shell:
```neo4j start
```
4. open an internet browser and open http://localhost:7474. 4. open an internet browser and open http://localhost:7474.
5. To visualize the whole pangenome, type this simple Cypher command in the browser: 5. To visualize the whole pangenome, type this simple Cypher command in the browser: `MATCH (n) RETURN n`
`MATCH (n) RETURN n` 6. Stop the Neo4j database server from the shell: `neo4j stop`
6. Stop the Neo4j database server from the shell: \ No newline at end of file
```neo4j stop
```
\ No newline at end of file
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