Genomic Read Matching and Annotation Pipeline (GRMAP)

A bioinformatics pipeline for matching sequencing reads to a reference genome and annotating the matched sequences with genomic features.

📌 Overview of the Workflow

1. Script 1: Read Matching & Extraction

   • Takes sequencing reads (from illumina_reads_X.fasta.gz) and matches them to a reference genome (hg38_xxx.fasta.gz).
   • Uses multi-threaded processing to improve speed.
   • Finds locations of matches in the reference genome and records:
     • Start & End positions
     • Strand orientation (Forward F / Reverse R)
     • Matched sequence
     • Upstream and downstream context (20 bp)
   • Outputs: matchedseqs.txt → A table of matched sequences and their genomic positions.

2. Script 2: Genomic Feature Annotation

   • Uses matchedseqs.txt from Script 1.
   • Loads multiple genomic feature files:
     • GFF3 (Gene annotation)
     • TSS file (Transcription Start Sites)
     • CpG island file (Methylation hotspots)
     • RepeatMasker file (Repetitive elements like SINEs, LINEs)
   • Annotates each matched sequence by:
     • Finding the closest gene and its type.
     • Checking if the sequence is in a CpG island.
     • Checking if the sequence overlaps with a repetitive element.
   • Outputs: matchedseqs_annotate.txt → An annotated version of matchedseqs.txt with additional biological context.

🔹 Summary of the Pipeline

Step	Script	Purpose	Output
1. Read Matching	match.pl	Matches sequencing reads to the reference genome	matchedseqs.txt
2. Genomic Annotation	annotate.pl	Annotates matched sequences with genes, CpG islands, and repeat elements	matchedseqs_annotate.txt

Benchmarking Details [match.pl] (2023)

Read Length	Query Size	Markers Found	Runtime	Memory Usage
40	1,000	511	2.94 min	334 MB
60	1,000	446	3.27 min	336 MB
80	1,000	415	3.83 min	337.5 MB
100	1,000	439	3.23 min	341 MB
100	10,000	4,280	33 min	341 MB

Benchmarking Details [match.pl] (Jan 2025)

Read Length	Query Size	Markers Found	Runtime	Memory Usage
40	1000	2590	0.03 min	198.16 MB
40	10000	39694	0.23 min	202.75 MB
40	100000	400556	2.18 min	248.42 MB
40	1000000	400556	2.22 min	248.42 MB
60	1000	1395	0.03 min	248.42 MB
60	10000	12669	0.23 min	248.42 MB
60	100000	129502	2.12 min	250.07 MB
60	1000000	129502	2.10 min	250.07 MB
80	1000	1092	0.03 min	250.07 MB
80	10000	9866	0.22 min	250.07 MB
80	100000	101426	2.11 min	253.08 MB
80	1000000	101426	2.10 min	253.08 MB
100	1000	867	0.03 min	253.08 MB
100	10000	8822	0.23 min	253.08 MB
100	100000	90293	2.14 min	256.41 MB
100	1000000	90293	2.13 min	256.41 MB

Author

Abhinav Mishra mishraabhinav36@gmail.com

License

This project is licensed under the MIT License.