How giuntalab/gcp-centeny works
GCP is a command-line toolkit for profiling centromeric DNA. Its documented workflow searches a FASTA sequence for the CENP-B-box motif, then uses the resulting motif locations for centeny visualization or one of three annotation models. A separate reads-retrieval command takes read-level motif data and pattern counts to select chromosome-specific reads. The README documents these command relationships; source excerpts were unavailable, so internal call details beyond the CLI dispatch are not inferred.
Main entry points: GCP.R Command dispatcher · chr17.t2t-chm13-v2.0.fa_NTTCGNNNNANNCGGGN.bed Motif locations · fuzznuc.sh Motif search · centeny.R Centeny mapping
Components 20
CLI dispatch
- Command dispatcher
R/GCP.R
Motif processing
- Motif search
R/fuzznuc.sh - Motif locations
output/chr17.t2t-chm13-v2.0.fa_NTTCGNNNNANNCGGGN.bed - Motif lengths
output/chr17.t2t-chm13-v2.0.fa_NTTCGNNNNANNCGGGN_length.tsv - Centeny mapping
R/centeny.R - Centeny annotations
output/centeny.bed
Annotation models
- Distance model
R/model1.R - CHM13 distances
file/chm13_model1.txt - Model 1 annotations
output/model1.bed - Monomer model
R/model2.R - Monomer reference
file/model2.txt - Model 2 annotations
output/model2.bed - K-pattern model
R/model3.R - Model 3 annotations
output/model3.bed
Read retrieval
- Specific read retrieval
R/reads_retrieval.R - Read motif data
test/ONT_100kb_2023_07_28_all_fasta_NTTCGNNNNANNCGGGN.bed - Pattern counts
output/pattern_counts_sliding1_k4.txt - Selected reads
output/chr17_specific_reads.txt
Other components
- Analyst
- Genome FASTA
test/chr17.t2t-chm13-v2.0.fa.gz
Connections 24
- Analyst → Command dispatcher: runs command
- Command dispatcher → Motif search: dispatches
- Command dispatcher → Centeny mapping: dispatches
- Command dispatcher → Distance model: dispatches
- Command dispatcher → Monomer model: dispatches
- Command dispatcher → K-pattern model: dispatches
- Command dispatcher → Specific read retrieval: dispatches
- Genome FASTA → Motif search: sequence input
- Motif search → Motif locations: writes locations
- Motif search → Motif lengths: writes lengths
- Motif locations → Centeny mapping: location input
- Motif lengths → Centeny mapping: length input
- Centeny mapping → Centeny annotations: writes annotations
- Motif locations → Distance model: location input
- CHM13 distances → Distance model: distance reference
- Distance model → Model 1 annotations: writes annotations
- Motif locations → Monomer model: location input
- Monomer reference → Monomer model: monomer reference
- Monomer model → Model 2 annotations: writes annotations
- Motif locations → K-pattern model: location input
- K-pattern model → Model 3 annotations: writes annotations
- Read motif data → Specific read retrieval: read input
- Pattern counts → Specific read retrieval: pattern input
- Specific read retrieval → Selected reads: writes selected reads