Crossroad fastAPI and CLI
A comprehensive tool for analyzing Simple Sequence Repeats (SSRs) in genomic data,
Features
- SSR comparative analysis of genomic data
- Relative abundance and Relative density
- Conserved, shared, and unique SSR motifs
- Gene-based SSR analysis
- Mutational hotspot detection
- Evolutionary analysis:SSR length variation with respect to time point
- Both Reference free and Reference-based comparison
- REST API support
Installation
Using pip
Contributors
- Dr. Preeti Agarwal (PhD & Senior Research Fellow)
- Dr. Jitendra Narayan (Principal Investigator)
- Pranjal Pruthi (Project Scientist, CSIR IGIB)
Institution
CSIR-Institute of Genomics and Integrative Biology Lab of Bioinformatics and Big Data analysis Mall Road, New Delhi - 110007, India
License
MIT License
Citation
If you use Crossroad in your research, please cite: [Citation information coming soon]
| Output File | With Reference ID | Without Reference ID |
|---|---|---|
| hssr_data.csv | 1. find_different_repeats() finds differences from reference 2. group_ssr_records_from_excluded() groups these differences 3. filter_hotspot_records() filters for variations 4. process_hssr_data() creates final HSSR data |
1. group_ssr_records() groups all SSRs 2. filter_hotspot_records() filters for variations 3. process_hssr_data() creates final HSSR data |
| ref_ssr_genecombo.csv (excluded_repeats) |
1. find_different_repeats() identifies differences from reference 2. Saves directly to file 3. Only created when reference ID is given |
Not created |
| all_variations.csv | 1. find_different_repeats() finds differences 2. group_ssr_records_from_excluded() processes these 3. Saves to file before filtering |
1. group_ssr_records() groups all SSRs 2. Saves to file before filtering |
| mutational_hotspots.csv | 1. Uses grouped excluded repeats 2. filter_hotspot_records() finds variations 3. Applies min_repeat_count and min_genome_count filters |
1. Uses grouped all SSRs 2. filter_hotspot_records() finds variations 3. Applies min_repeat_count and min_genome_count filters |
Each file in simple terms:
hssr_data.csv:
- Final output containing hotspot SSRs
- With reference: Only includes variations different from reference
- Without reference: Includes all variations meeting criteria
ref_ssr_genecombo.csv (excluded_repeats):
- Only created when using reference ID
- Lists all SSRs that are different from reference genome
- Raw differences before processing
all_variations.csv:
- With reference: All variations of different SSRs from reference
- Without reference: All variations of all SSRs
- Intermediate file before filtering
mutational_hotspots.csv:
-
Contains filtered hotspots meeting criteria
-
Uses min_repeat_count and min_genome_count
-
With reference: Only from differences
-
Without reference: From all SSRs
2 maintainers
Metadata
2 maintainers
Release files for crossroad-cli 0.3.5
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| crossroad_cli-0.3.5-py3-none-any.whl | Python 3 | none | any | Details for crossroad_cli-0.3.5-py3-none-any.whl |
Total release size: 187.0 kB
Release files / crossroad_cli-0.3.5.tar.gz
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