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# Documentation for `seqproc` | ||
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`seqproc` is a program for interpreting and transforming sequencing data | ||
according to the extended fragment geometry description language (EFGDL). | ||
In fact, currently, the `seqproc` executable is a rather thin wrapper around | ||
the underlying `seqproc` library, whose main purpose it to accept an input | ||
stream of reads (consisting of single-end or paired-end reads) and an EFGDL | ||
specification, and to transform the input reads into the desired output format | ||
according to the specification. | ||
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Thus, most of the important information regarding `seqproc` actually pertains | ||
to the EFGDL, which has its own documentation. For detailed documentation | ||
describing EFGDL, please visit the EFGDL specification documentation | ||
[here](https://efgdl-spec.readthedocs.io/en/latest/). | ||
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## Using `seqproc` | ||
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The `seqproc` program is an executable that exposes a single command that takes | ||
several command line arguments. You can pass the `-h` or `--help` flag to `seqproc` | ||
to see the various command line arguments and their descriptions. | ||
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$ ./target/release/seqproc -h | ||
General puprose sequence preprocessor | ||
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Usage: seqproc [OPTIONS] --geom <GEOM> --file1 <FILE1> --file2 <FILE2> | ||
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Options: | ||
-g, --geom <GEOM> EFGDL string | ||
-1, --file1 <FILE1> r1 fastq file | ||
-2, --file2 <FILE2> r2 fastq file | ||
-o, --out1 <OUT1> r1 out fastq file [default: ] | ||
-w, --out2 <OUT2> r2 out fastq file [default: ] | ||
-t, --threads <THREADS> number of threads to use [default: 1] | ||
-a, --additional <ADDITIONAL>... | ||
-h, --help Print help | ||
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site_name: Documentation for seqproc | ||
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name: material | ||
palette: | ||
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# Palette toggle for light mode | ||
- scheme: default | ||
toggle: | ||
icon: material/brightness-7 | ||
name: Switch to dark mode | ||
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# Palette toggle for dark mode | ||
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toggle: | ||
icon: material/brightness-4 | ||
name: Switch to light mode |