@@ -134,13 +134,13 @@ Add the path to the java archive of PanTools, located in the /dist subdirectory
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@@ -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.
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@@ -153,14 +153,8 @@ Add the path to the java archive of PanTools, located in the /dist subdirectory
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@@ -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```