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name : malt_run
description : MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
keywords :
- malt
- alignment
- metagenomics
- ancient DNA
- aDNA
- palaeogenomics
- archaeogenomics
- microbiome
tools :
- malt :
description : A tool for mapping metagenomic data
homepage : https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
documentation : https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
tool_dev_url : None
doi : "10.1038/s41559-017-0446-6"
licence : [ 'GPL v3' ]
input :
- fastqs :
type : file
description : Input FASTQ files
pattern : "*.{fastq.gz,fq.gz}"
- mode :
type : string
description : Program mode
pattern : 'Unknown|BlastN|BlastP|BlastX|Classifier'
- index :
type : directory
description : Index/database directory from malt-build
pattern : '*/'
output :
- version :
type : file
description : File containing software version
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pattern : "versions.yml"
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- rma6 :
type : file
description : MEGAN6 RMA6 file
pattern : "*.rma6"
- sam :
type : file
description : Alignment files in Tab, Text or MEGAN-compatible SAM format
pattern : "*.{tab,txt,sam}"
- log :
type : file
description : Log of verbose MALT stdout
pattern : "malt-run.log"
authors :
- "@jfy133"