- Livermore, CA
- http://john.didion.net
- @jdidion
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bgen Public
Library and command line tools for working with BGEN files
Rust MIT License UpdatedNov 14, 2025 -
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atropos Public
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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pest-test Public
Testing framework for pest parser (similar to `tree-sitter test`)
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rust-htslib Public
Forked from rust-bio/rust-htslibThis library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
Rust MIT License UpdatedApr 28, 2025 -
xphyle Public
Python library that facilitates opening, reading, and writing files (and file-like entities like URLs and streams) agnostic of compression format. (production)
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io-streams Public
Forked from sunfishcode/io-streamsUnbuffered and unlocked I/O streams
Rust Other UpdatedAug 20, 2024 -
pairwise-alignment Public
Catalogue of pairwise alignment algorithms and benchmarks
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pytest-workflow Public
Forked from LUMC/pytest-workflowConfigure workflow/pipeline tests using yaml files.
Python GNU Affero General Public License v3.0 UpdatedMay 29, 2024 -
release-plz Public
Forked from release-plz/release-plzPublish Rust crates from CI with a Release PR.
Rust Apache License 2.0 UpdatedApr 4, 2024 -
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MultiQC Public
Forked from MultiQC/MultiQCAggregate results from bioinformatics analyses across many samples into a single report.
Python GNU General Public License v3.0 UpdatedMar 8, 2024 -
cwl-v1.2 Public
Forked from common-workflow-language/cwl-v1.2Released CWL v1.2 specification
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tree-sitter-wdl Public
Tree-sitter grammar for WDL (Workflow Description Language)
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wdl-rs Public
Rust parser for Workflow Description Language (WDL)
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read-structure Public
Forked from fulcrumgenomics/read-structureRust MIT License UpdatedJun 1, 2023 -
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subby Public
Python subprocesses simplified.
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tree-sitter Public
Forked from tree-sitter/tree-sitterAn incremental parsing system for programming tools
Rust MIT License UpdatedMar 13, 2023 -
seq_geom_parser Public
Forked from COMBINE-lab/seq_geom_parserTesting out rust parsing of single-cell library geometry specifications
Rust BSD 3-Clause "New" or "Revised" License UpdatedMar 8, 2023 -
pest-wdl Public
Pest parser grammar for Workflow Description Language (WDL)
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wdlTools Public
Forked from dnanexus/wdlToolsWDL tools for parsing, type-checking, and more
Scala Apache License 2.0 UpdatedDec 22, 2022 -
tree-sitter-python Public
Forked from tree-sitter/tree-sitter-pythonPython grammar for tree-sitter
JavaScript MIT License UpdatedDec 8, 2022 -
cachier Public
Forked from python-cachier/cachierPersistent, stale-free, local and cross-machine caching for Python functions.
Python MIT License UpdatedDec 2, 2022 -
pytest-datadir-nng Public
The *next* next generation of python-datadir
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syncmers Public
Forked from jguhlin/syncmersLibrary for finding syncmers from &[u8] in rust
Rust MIT License UpdatedOct 18, 2022 -
streammd Public
Forked from delocalizer/streammdSingle-pass probabilistic duplicate marking of alignments with a Bloom filter.
C++ MIT License UpdatedOct 18, 2022





