This piece of code converts a MAF-File produced by LAST into a DIAMOND specific file format called DAA-File, which can then be loaded into MEGAN for example.
Given a query file together with a LAST database you basically have to conduct the following steps:
- Run LAST mapping the query on a database by reporting a MAF file.
- Convert the MAF file into a DAA file by using this tool.
- Run MEGAN for first meganizing the DAA file and then visualizing the assigned taxa.
Get the current version from here.
| Parameter | Description |
|---|---|
| -i, --in | sets path to MAF-File (can also be piped in, no gzip allowed here) |
| -r, -- reads | sets path to query-file in FASTA or FASTQ format (can also be gzipped) |
| -o, --out | sets path of the reported DAA-File |
| Parameter | Description |
|---|---|
| -top, --topPercent | sets top percent of reads kept during filtering (default: 10.0) |
| --p, --procs | sets number of used processors (default: maximal number) |
| Parameter | Description |
|---|---|
| -ps, --streamingProcs | sets number of used processors while input is piped-in (default: 1) |
| -cs, --chunkSize | sets chunk-size of temporary MAF files (default: 500mb) |
| --t, --tmp | sets folder for temporary files (default: parent folder of the resulting DAA-File) |
| Parameter | Description |
|---|---|
| -v, --verbose | sets verbose mode reporting numbers of reads/references/alignments being analyzed |
| -h, --help | shows program usage and quits |
Either the MAF-file is directly specfied, like
java -jar DAA_Converter.jar -m <maf-file> -q <read-file>
or the MAF-file is piped in from LAST, like
lastal -P8 -F15 <last-db> <read-file> | java -jar DAA_Converter.jar -q <read-file>
Notice that the latter variant of calling the converter has the advantage that no big MAF-file has to be stored on disk. Here, each chunk of the MAF-file is directly filtered and then compressed into a DAA-file. In the end all the resulting DAA-files are merged into one single DAA-File.