crossroad-cli 0.3.0

A tool for analyzing SSRs in genomic data

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