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nf-core/amps
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malt
MaltExtract
HOPS
amps
alignment
metagenomics
ancient DNA
aDNA
palaeogenomics
archaeogenomics
microbiome
authentication
damage
edit distance
post Post-processing
visualisation
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Post-processing script of the MaltExtract component of the HOPS package
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nf-core/argnorm
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amr
antimicrobial resistance
arg
antimicrobial resistance genes
genomics
metagenomics
normalization
drug categorization
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Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).
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nf-core/biomformat/convert
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biom
feature table
formatting
conversion
amplicon sequences
metagenomics
metatranscriptomics
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Convert biom table to different format.
Conversion between text tab-delimited, BIOM-v1 (JSON), and BIOM-v2 (HDF5) formats are supported
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nf-core/bracken/bracken
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bracken
metagenomics
abundance
kraken2
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Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
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nf-core/bracken/combinebrackenoutputs
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bracken
metagenomics
postprocessing
reporting
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Combine output of metagenomic samples analyzed by bracken.
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nf-core/centrifuge/build
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database
metagenomics
build
db
fasta
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Build centrifuge database for taxonomic profiling
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nf-core/centrifuge/centrifuge
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classify
metagenomics
fastq
db
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Classifies metagenomic sequence data
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nf-core/centrifuge/kreport
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classify
metagenomics
fastq
db
report
kraken
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Creates Kraken-style reports from centrifuge out files
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nf-core/centrifuger/build
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metagenomics
taxonomic-classification
database-build
centrifuger
centrifuge
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Build centrifuger database for taxonomic profiling
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nf-core/centrifuger/centrifuger
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metagenomics
classification
centrifuger
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Classification of sequencing reads using the Centrifuger tool.
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nf-core/centrifuger/quantification
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metagenomics
quantification
Centrifuger
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Quantification (taxonomic profiling) of Centrifuger model
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nf-core/clame
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sort
genomics
binning
metagenomics
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binning of metagenomic sequences
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nf-core/cleanifier/download
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download
index
metagenomics
contamination removal
microbiome
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Download human reference index
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nf-core/cleanifier/filter
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contamination removal
metagenomics
microbiome
filter
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Fast, lightweight contamination removal from microbiome data (FASTQ) using a probabilistic Cuckoo filter or Cuckoo hash table index
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nf-core/cleanifier/index
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index
genomics
metagenomics
contamination removal
microbiome
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Builds a Cuckoo filter or Cuckoo hash table index from reference sequences (FASTA/FASTQ) for fast contamination removal.
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nf-core/comebin/runcomebin
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metagenomics
binning
clustering
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Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning
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nf-core/concoct/concoct
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contigs
fragment
mags
binning
concoct
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