Process Details¶

1. Matching Reads¶

Script: scripts/match.pl

Inputs:

Input	Description
reads	Sample FASTA (e.g. data/reads/illumina_reads_<length>.fasta.gz)
reference	Genome FASTA (e.g. data/ref/hg38_partial.fasta.gz)

Output:
- results/{sample}.matched (tab-delimited list of matched regions)

Description:
It takes each input read set and searches against the reference, emitting one line per successful match with coordinates and basic alignment metrics.

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Benchmarking¶

[match.pl] (Nov 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

[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

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2. Annotating Matches¶

Script: scripts/annotate.pl

Inputs:

File	Description
results/{sample}.matched	Matched read output from previous step
hg38_chr1_geneannotation.gff3.gz	Gene features
hg38_chr1_tss.txt.gz	Transcription start sites
hg38_cpg.txt.gz	CpG locations
hg38_repeatmasker.bed.gz	Repetitive elements

Output:
- results/{sample}.annotated (tab-delimited, with annotation columns)

Description:
It enriches each match record by querying overlap with gene models, TSS positions, CpG sites, and repeat regions.
The output adds columns for:

• Gene ID and feature type
• Distance to nearest TSS
• CpG count within the matched interval
• Overlap with repeat elements