1 unstable release
0.1.0 | Feb 11, 2022 |
---|
#744 in Science
13KB
160 lines
splitp
Streaming SPLiT-seq read pre-processing in Rust. Currently, this is just a Rust implementation of the Perl pre-processing script by @jeremymsimon here. In the future, capabilities may expand / become more general.
The raison d'etre of the program is simply to perform equivalent processing to the custom Perl script above, but much faster. To that end, here's a small benchmark on a set of 10,000,000 SPLiT-seq v2 reads. This is on a 2016 MacBook Pro 2.9 GHz Quad-Core Intel Core i7, 16 GB 2133 MHz LPDDR3 (but both programs are using a single thread).
program | runtime |
---|---|
Perl script | 2m 48.6s |
splitp | 5.7s |
splitp (pipe to /dev/null ) |
3.7s |
Usage
The splitp
program takes several arguments. The usage can be printed
from the command line using splitp -h
.
USAGE:
splitp [OPTIONS] --read-file <READ_FILE> --bc-map <BC_MAP> --start <START> --end <END>
OPTIONS:
-b, --bc-map <BC_MAP> the map of oligo-dT to random hexamers
-e, --end <END> end position of the random barcode
-h, --help Print help information
-o, --one-hamming consider 1-hamming distance neighbors of random hexamers
-r, --read-file <READ_FILE> the input R2 file
-s, --start <START> start position of the random barcode
-V, --version Print version information
Please take note that splitp
writes the output (processed reads) to stdout, so that the
output can be directly piped to an input stream of another program (e.g. directly
to alevin-fry
via process substitution). This
also means, if you want to store the processed reads on disk, you can pipe the results directly
to gzip to compress them e.g.:
splitp -r reads.fq -b oligo_hex_bc_mapping.txt -s 87 -e 94 -o | gzip > reads.fq.gz
Notes
The input oligo-dT to random-mer mapping must be provided in a two-column tab-separated file.
Further, the first row of the file must be a comment starting with the #
character.
Limitations / differences
- Currently, random hexamers can only be searched at a Hamming distance of 0 or 1.
- If the barcode being considered for replacement (BC1) has
N
characters in it, they are all replaced withA
before lookup in the table of random hexamer hamming neighbors. If there is more than oneN
, this may result in slightly different behavior than the Perl script.
Dependencies
~4.5MB
~71K SLoC