How jenniferlu717/krakentools works
KrakenTools is a command-line toolkit for downstream processing of Kraken-family and Bracken metagenomic classification results. Users can extract reads by taxonomy ID, combine and convert reports, calculate diversity metrics, filter Bracken results, and construct reports from Kraken output and taxonomy data. The graph preserves these as distinct, mostly independent workflows rather than implying one mandatory pipeline. Edges reflect documented inputs, outputs, and conversions; unsampled implementations are represented by their exact script paths without inferring additional internal calls.
Main entry points: fix_unmapped.py Map accessions · extract_kraken_reads.py Extract reads · make_kreport.py Build Kraken report · combine_kreports.py Combine reports
Components 32
Read extraction
- Extract reads
extract_kraken_reads.py
Report processing
- Combine reports
combine_kreports.py - Convert to Krona
kreport2krona.py - Convert to MetaPhlAn
kreport2mpa.py - Combine MetaPhlAn
combine_mpa.py - Filter Bracken output
filter_bracken.out.py
Taxonomy tools
- Build taxonomy
make_ktaxonomy.py - Build Kraken report
make_kreport.py - Map accessions
fix_unmapped.py
Abundance analysis
- Alpha diversity
DiversityTools/alpha_diversity.py - Beta diversity
DiversityTools/beta_diversity.py
Other components
- KrakenTools user
- Kraken results
- FASTA/FASTQ reads
- Extracted reads
- Kraken reports
- Combined report
- Krona-format report
- MetaPhlAn-format report
- Combined MetaPhlAn report
- Bracken output
- Filtered Bracken output
- Bracken abundance input
- Alpha diversity metrics
- Community abundance inputs
- Bray-Curtis matrix
- NCBI taxonomy files
- Condensed taxonomy
- Accession IDs
- Accession-to-taxid maps
- Mapped accessions
- Unmapped accessions
Connections 37
- KrakenTools user → Extract reads: runs
- Kraken results → Extract reads: reads classifications
- FASTA/FASTQ reads → Extract reads: provides reads
- Extract reads → Extracted reads: writes extracted reads
- KrakenTools user → Combine reports: runs
- Kraken reports → Combine reports: combines
- Combine reports → Combined report: writes combined report
- KrakenTools user → Convert to Krona: runs
- Kraken reports → Convert to Krona: converts report
- Convert to Krona → Krona-format report: writes Krona format
- KrakenTools user → Convert to MetaPhlAn: runs
- Kraken reports → Convert to MetaPhlAn: converts report
- Convert to MetaPhlAn → MetaPhlAn-format report: writes MetaPhlAn format
- KrakenTools user → Combine MetaPhlAn: runs
- MetaPhlAn-format report → Combine MetaPhlAn: combines reports
- Combine MetaPhlAn → Combined MetaPhlAn report: writes combined report
- KrakenTools user → Filter Bracken output: runs
- Bracken output → Filter Bracken output: filters taxids
- Filter Bracken output → Filtered Bracken output: writes filtered output
- KrakenTools user → Build taxonomy: runs
- NCBI taxonomy files → Build taxonomy: provides taxonomy data
- Build taxonomy → Condensed taxonomy: writes taxonomy
- KrakenTools user → Build Kraken report: runs
- Kraken results → Build Kraken report: provides classifications
- Condensed taxonomy → Build Kraken report: provides taxonomy
- Build Kraken report → Kraken reports: writes report
- KrakenTools user → Map accessions: runs
- Accession IDs → Map accessions: provides IDs
- Accession-to-taxid maps → Map accessions: provides mappings
- Map accessions → Mapped accessions: writes mapped IDs
- Map accessions → Unmapped accessions: writes unresolved IDs
- KrakenTools user → Alpha diversity: runs
- Bracken abundance input → Alpha diversity: provides abundances
- Alpha diversity → Alpha diversity metrics: calculates indices
- KrakenTools user → Beta diversity: runs
- Community abundance inputs → Beta diversity: provides communities
- Beta diversity → Bray-Curtis matrix: calculates dissimilarity