Modern DNA sequencing is used as a readout for diverse assays, with the count of aligned sequences, or "read depth", serving as the quantitative signal for many underlying cellular phenomena. Despite wide use and thousands of datasets, existing formats used for the storage and analysis of read depths are limited with respect to both size and speed. For example, it is faster to recalculate sequencing depth from an alignment file than it is to analyze the text output from that calculation. We sought to improve on existing formats such as BigWig and compressed BED files by creating the Dense Depth Data Dump (D4) format and tool suite. The D4 format is adaptive in that it profiles a random sample of aligned sequence depth from the input BAM or CRAM file to determine an optimal encoding that minimizes file size, while also enabling fast data access. We show that D4 uses less disk space for both RNA-Seq and whole-genome sequencing and offers 3 to 440 fold speed improvements over existing formats for random access, aggregation and summarization for scalable downstream analyses that would be otherwise intractable.
- From CRAM/BAM file
d4utils create -Azr ../data/hg19.fa.gz.fai ../data/hg002.cram /tmp/hg002.d4
- From BigWig file
d4utils create -z input.bw output.d4
- From a BedGraph file
d4utils create -z -g hg19.genome input.bedgraph output.d4
$ d4utils view ../data/hg002.d4 | head -n 10
chr1 0 9998 0
chr1 9998 9999 6
chr1 9999 10000 9
chr1 10000 10001 37
chr1 10001 10002 59
chr1 10002 10003 78
chr1 10003 10004 100
chr1 10004 10005 116
chr1 10005 10006 130
chr1 10006 10007 135
$ d4utils stat ../data/hg002.d4
chr1 0 249250621 27.075065016588262
chr10 0 135534747 31.59483947684648
chr11 0 135006516 25.970025943044114
chr11_gl000202_random 0 40103 14.47213425429519
chr12 0 133851895 25.80992053194316
chr13 0 115169878 24.18613685602758
chr14 0 107349540 24.25194093053403
chr15 0 102531392 23.04176524785697
chr16 0 90354753 28.106620932271266
chr17 0 81195210 25.58382477242192
...
To build d4
, Rust toolchain is required. To install Rust toolchain,
please run the following command and follow the prompt to complete the
Rust installation.
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
gcc
or clang
is required to build htslib
embeded with the d4
library.
For details, please check the htslib repository.
Normally, the build step is quite easy. Just
# For Debug Build
cargo build
# For Release Build
cargo build --release
And it will produce the d4utils
binary which you can find at either
target/debug/d4utils
or target/release/d4utils
depends on which build mode
you choose.
You can choose to install the d4utils bindary by running
cargo install --path .
Or you can choose install from crates.io:
cargo install d4utils