PanDepth, an ultrafast and efficient genomic tool for coverage calculation
The PanDepth article has been published in Briefings in Bioinformatics . Please cite this article if possible.
PMID: 38701418 DOI: 10.1093/bib/bbae197
wget -c https://github.com/HuiyangYu/PanDepth/releases/download/v2.25/PanDepth-2.25-Linux-x86_64.tar.gz
tar zvxf PanDepth-2.25-Linux-x86_64.tar.gz
cd PanDepth-2.25-Linux-x86_64
./pandepth -h
git clone https://github.com/HuiyangYu/PanDepth.git
cd PanDepth
make
cd bin
./pandepth -h
Usage: pandepth -i in.bam [-g gene.gff | -b region.bed] -o outPrefix
Input/Output options:
-i <str> input of sam/bam/cram/paf or #.list file
-o <str> prefix of output file
Target options:
-g <str> input gff/gtf file for gene region
-f <str> gff/gtf feature type to parse, CDS or exon [CDS]
-b <str> input bed file for list of regions
-w <int> windows size (bp)
-a output all the site depth
Filter options:
-q <int> min mapping quality [0]
-x <int> exclude reads with any of the bits in FLAG set [1796]
Other options:
-t <int> number of threads [3]
-r <str> reference genome file for cram decode or GC parse
-c enable the calculation of GC content (requires -r)
-h show this help [v2.25]
pandepth -i test.bam -o test1
The output file, named "test1.chr.stat.gz", follows the following format:
#Chr Length CoveredSite TotalDepth Coverage(%) MeanDepth
Chr01 332615375 331690145 16945298412 99.72 50.95
Chr02 177319215 176853774 8368043949 99.74 47.19
Chr03 289790774 288837978 14143309698 99.67 48.81
Chr04 248932513 248384761 11741149343 99.78 47.17
Chr05 254874144 253897405 12548725234 99.62 49.23
Chr06 253233553 252488900 11854653791 99.71 46.81
Chr07 266382521 265595425 12873116925 99.70 48.33
Chr08 174326481 173874883 8437159467 99.74 48.40
Chr09 278410012 277664711 13068321410 99.73 46.94
pandepth -i test.bam -g test.gff -o test2
The output file, named 'test2.gene.stat.gz', follows the following format:
#Chr Start End GeneID Length CoveredSite TotalDepth Coverage(%) MeanDepth
Chr01 16621 30840 Caz01g00010.1 819 819 38297 100.00 46.76
Chr01 66931 67440 Caz01g00030.1 510 510 23804 100.00 46.67
Chr01 131205 142847 Caz01g00040.1 3357 3357 161705 100.00 48.17
Chr01 147579 148601 Caz01g00050.1 1023 1023 59443 100.00 58.11
Chr01 165397 166582 Caz01g00060.1 297 297 13764 100.00 46.34
Chr01 180956 190456 Caz01g00070.1 1602 1602 77279 100.00 48.24
Chr01 193092 194509 Caz01g00080.1 411 411 23014 100.00 56.00
Chr01 230152 236238 Caz01g00090.1 1869 1869 94470 100.00 50.55
Chr01 245657 246295 Caz01g00100.1 510 510 29332 100.00 57.51
pandepth -i test.bam -b test.bed -o test3
The output file, named 'test3.bed.stat.gz', follows the following format:
#Chr Start End RegionID Length CoveredSite TotalDepth Coverage(%) MeanDepth
Chr01 16621 16662 Chr01_16621_16662 42 42 1935 100.00 46.07
Chr01 16838 16947 Chr01_16838_16947 110 110 5522 100.00 50.20
Chr01 17445 17520 Chr01_17445_17520 76 76 3387 100.00 44.57
Chr01 28409 28474 Chr01_28409_28474 66 66 3901 100.00 59.11
Chr01 29747 29917 Chr01_29747_29917 171 171 5141 100.00 30.06
Chr01 30102 30289 Chr01_30102_30289 188 188 8394 100.00 44.65
Chr01 30403 30532 Chr01_30403_30532 130 130 7786 100.00 59.89
Chr01 30805 30840 Chr01_30805_30840 36 36 2231 100.00 61.97
Chr01 66931 67440 Chr01_66931_67440 510 510 23804 100.00 46.67
The 'RegionID' is automatically generated in the output results and does not need to exist in the input BED file. The BED file only needs three columns, namely Chr/Contig, Start, and End.
pandepth -i test.bam -w 100 -o test4
The output file, named 'test4.win.stat.gz', follows the following format:
#Chr Start End Length CoveredSite TotalDepth Coverage(%) MeanDepth
Chr01 1 100 100 0 0 0.00 0.00
Chr01 101 200 100 0 0 0.00 0.00
Chr01 201 300 100 26 26 26.00 0.26
Chr01 301 400 100 12 12 12.00 0.12
Chr01 401 500 100 65 275 65.00 2.75
Chr01 501 600 100 100 770 100.00 7.70
Chr01 601 700 100 100 679 100.00 6.79
Chr01 701 800 100 33 93 33.00 0.93
Chr01 801 900 100 0 0 0.00 0.00
The species used for software performance evaluation is Capsicum annuum, with a genome size of 3 Gb, 33688 genes, and 175274 exons. The software versions employed are as follows: Samtools (v1.16.1), BEDTools (v2.31.0), Sambamba (v1.0.0), Mosdepth (v0.3.5), Megadepth (v1.2.0), BamToCov (v2.7.0), and PanDepth (v2.19). All evaluations were conducted on nodes equipped with 52 cores and 192 GB of memory, repeated 10 times, utilizing the SLURM job scheduling system.
The computation time comparison of seven tools for calculating genome coverage using different numbers of threads with 150 Gb of sequencing reads.
The computation time comparison of seven tools for calculating exon coverage using different numbers of threads with 150 Gb of sequencing reads.
The memory requirements comparison of seven tools for calculating genome coverage using different numbers of threads with 150 Gb of sequencing reads.
The memory requirements comparison of seven tools for calculating exon coverage using different numbers of threads with 150 Gb of sequencing reads.
The statistical results of PanDepth on depth and coverage are completely consistent with samtools depth (version >=1.10).
PanDepth supports both short reads and long reads of types HIFI/CLR/ONT.
PanDepth supports alignment files in SAM, BAM, CRAM, PAF formats. Additionally, PAF files can be compressed with 'gz' extension. However, in the PAF format alignment files, it is required to include the CIGAR tag. If you perform the alignment using minimap2 or winnowmap, you can add this tag using the '-c' parameter.
When the input file is in PAF format, PanDepth will check if the filtering flag specified by '-x' contains the '0x100' flag (secondary alignment). If these flags are present in the alignments, the corresponding alignment regions will be filtered out.
PanDepth supports statistical analysis of genome-to-genome alignments, but the input file needs to be in PAF format with the CIGAR tag included.
5.5 Does PanDepth require index files for the corresponding alignment files during the analysis process?
If you provide a BAM or CRAM file, sorting and indexing are not necessary. However, if you have sorted BAM or CRAM files along with their corresponding index files, PanDepth can utilize multi-threading to accelerate the computation.
PanDepth's single-threaded computation is also extremely fast.
If your alignment files are intended solely for coverage and depth statistics, especially for assessing the quality of assembled genomes, we recommend avoiding sorting during the generation of BAM or CRAM files. This is because sorting large alignment files using tools like 'samtools sort' can be extremely time-consuming.
In PanDepth, the '-x' parameter is set to 1796 by default, which filters out reads with flags indicating unmapped, secondary alignment, not passing quality controls, PCR or optical duplicate. This default filtering is consistent with that of 'samtools depth'.
If you wish to apply other types of filtering, you can select specific filters on this webpage (https://broadinstitute.github.io/picard/explain-flags.html) and pass the generated value after 'SAM Flag:' to the '-x' option.
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This project is licensed under the MIT License - see the LICENSE file for details