Testing on long reads

Speed measures

The speed test is performed via hyperfine:

hyperfine \
  "bin/bamtocov $FILE" \
  "megadepth --coverage --longreads $FILE" \
  "mosdepth -x /tmp/x $FILE" \
  --max-runs 3 --export-markdown $FILE.md
  

Datasets

Fungal dataset

The alignment of whole genome shotgun reads coming from a unicellular fungus sequences with MinION in our laboratory is available in the Zenodo dataset accompanying the paper.

wget -O cpara-ont.bam "https://zenodo.org/record/5636944/files/cpara-ont-noseq.bam?download=1"
  

Human sample

SRR13615770, from the study Cas9 targeted enrichment of mobile elements using nanopore sequencing is composed by 123,254 reads.

# Download reference
wget -O db/hg19.fa.gz http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.fa.masked.gz
# Download sample
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR136/070/SRR13615770/SRR13615770_1.fastq.gz \
  -o SRR13615770_L1Hs_MinION_1.fastq.gz

# Select reads > 2500bp
seqfu cat -m 2500 SRR13615770_L1Hs_MinION_1.fastq.gz | gzip -c > SRR13615770_L1Hs_MinION_1.min2500.fastq.gz

# Map 
minimap2 -ax map-ont -t 4 db/hg19.fa.gz SRR13615770_L1Hs_MinION_1.min2500.fastq.gz | \
  samtools view -bS | samtools sort -o SRR13615770.bam -
  

Benchmark result

hyperfine \
  "bin/bamtocov $FILE" \
  "megadepth --coverage --longreads $FILE" \
  "mosdepth -x /tmp/x $FILE" \
  --max-runs 2 --export-markdown $FILE.md
  

Results

SRR13615770_L1Hs_MinION_1 (full sample)

Command	Mean [s]	Min [s]	Max [s]	Relative
`bin/bamtocov SRR13615770_L1Hs_MinION_1.bam`	32.357 ± 0.261	32.172	32.541	1.00
`megadepth --coverage --longreads SRR13615770_L1Hs_MinION_1.bam`	46.115 ± 0.954	45.440	46.789	1.43 ± 0.03
`mosdepth -x /tmp/x SRR13615770_L1Hs_MinION_1.bam`	92.359 ± 5.448	88.506	96.211	2.85 ± 0.17

SRR13615770_2500bp (size selection: > 2,500 bp)

Command	Mean [s]	Min [s]	Max [s]	Relative
`bin/bamtocov SRR13615770.bam`	29.113 ± 0.121	28.981	29.219	1.00
`megadepth --coverage --longreads SRR13615770.bam`	43.366 ± 0.327	42.994	43.607	1.49 ± 0.01
`mosdepth -x /tmp/x SRR13615770.bam`	86.483 ± 2.312	83.878	88.293	2.97 ± 0.08

Fungus LR

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`bin/bamtocov _test/cpara-ont-noseq.bam`	310.5 ± 23.0	275.5	339.0	1.00
`megadepth --coverage --longreads _test/cpara-ont-noseq.bam`	557.4 ± 13.5	540.5	572.7	1.80 ± 0.14
`mosdepth -x /tmp/x _test/cpara-ont-noseq.bam`	792.5 ± 176.9	654.5	1092.7	2.55 ± 0.60