show |
X |
Show user-related goals. |
showall |
X |
Show user-related and most internal goals. |
genall |
X |
Generate the k-mer matching database and also the filtering database with respect to the given project. |
clear |
X |
Clear the folders csv, db and krakenout of a project. This will delete all files the respective folders! |
db |
X |
Generate the database for k-mer matching respect to the given project. |
dbinfo |
X |
Write information about a project's database content to a CSV file. |
db2fastq |
X |
Generate fastq files from the database. A respective fastq file will contain all k-mers specifically associated with a single tax id from the database where each k-mer is represented by a read consisting of k bases. Respective fastq files will be stored in <base dir>/projects/<project_name>/fastq with the file name format <project_name>_db2fastq_<taxid>.fastq.gz. The command line option tx serves at selecting the corresponding tax ids for the fastq files to be generated. If the option is omitted, then fastq files for all tax ids from the database will be generated. |
index |
X |
Generate a filtering database with respect to a given project. |
match |
X |
Analyze fastq files as given by the -f or -m option. The resulting CSV file(s) will be stored in <base dir>/projects/<project_name>/csv unless specified otherwise via the -r option. |
matchlr |
X |
Same as match but without doing read classification. This corresponds to the configuration setting classifyReads=false. |
filter |
X |
Filter fastq files as given by the -f or -m option. The resulting filtered fastq file(s) filtered_... will be stored under <base dir>/projects/<project_name>/fastq/ unless specified otherwise via the -r option. |
commonsetup |
|
Create data folders in <base dir>/common including common itself. |
setup |
|
Create data folders in <base dir>/<project>. |
taxdownload |
|
Download the taxonomy. |
taxtree |
|
Load the taxonomy into memory. |
taxnodes |
|
Compute the taxids for the project's database. |
refseqrelease |
|
Download the RefSeq release number. |
refseqcat |
|
Download the RefSeq release catalog files. |
checksummap |
|
Load MD5 checksums for RefSeq files into memory |
categories |
|
Load the RefSeq category names as requested for the project's database. |
refseqfna |
|
Download the genomic files from RefSeq for the requested categories. |
accmapsize |
|
Compute the number of RefSeq accession entries to be kept in memory. |
accmap |
|
Load the required RefSeq accession entries into memory. |
taxfromgenbank |
|
Determine for tax ids for which additional fasta files from Genbank should be downloaded. |
assemblydownload |
|
Download Genbank's assembly catalog file. |
fastasgenbank |
|
Determine the fasta files to be downloaded from Genbank. |
fastasgenbankdl |
|
Download the requested fasta files from Genbank. |
adddownloads |
|
Download additionally requested fasta files. |
addfastas |
|
Associate additional fasta files with tax ids in memory. |
fillsize |
|
Precompute the number of k-mers for the project's database. |
tempindex |
|
Fill the temporary bloom index with k-mers. |
filldb |
|
Fill the database with k-mers. |
tempdb |
|
Save temporary database. |
loadtempdb |
|
Load the temporary database into memory. |
updatedb |
|
Update the temporary database with regard to least commonn ancestors of k-mers. |
loaddb |
|
Load the matching database into memory. |
fillindex |
|
Fill the filtering database with k-mers. |
loadindex |
|
Load the filtering database into memory. |
db2fastqtaxids |
|
Determine tax ids for the goal db2fast from the command line argument. |
fastqmap |
|
Determine the fastq mapping from command line arguments. |
fastqmaptransform |
|
Transform URLs of fastq files to be downloaded to local paths. |
fastqdownload |
|
Download fastq files given via URLs as requested. |
krakenres |
|
For internal use (to invoke kraken). |