ggcat
Compacted and colored de Bruijn graph construction and querying
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Download Latest Version (.zip)- ci.yml
- release.yml
- main.rs
- Cargo.toml
- lib.rs
- utils.rs
- Cargo.lock
- Cargo.toml
- lib.rs
- Cargo.toml
- hashmap.rs
- sorting.rs
- final_executor.rs
- lib.rs
- map_processor.rs
- sorting.rs
- structs.rs
- unitigs_extender.rs
- Cargo.toml
- lib.rs
- rewrite_bucket.rs
- Cargo.toml
- mappings_loader.rs
- maximal_hash_entry.rs
- maximal_unitig_index.rs
- compute_matchtigs.rs
- eulertigs.rs
- extend_unitigs.rs
- lib.rs
- maximal_unitig_links.rs
- Cargo.toml
- .gitignore
- main.cc
- Makefile
- ggcat-cpp-bindings.hh
- ggcat.hh
- ggcat.cc
- .gitignore
- Makefile
- lib.rs
- build.rs
- Cargo.toml
- cmd_rewrite.rs
- benchmarks.rs
- cmd_utils.rs
- main.rs
- Cargo.lock
- Cargo.toml
- graph_querying.rs
- multifile_building.rs
- multiple.rs
- single.rs
- graph.rs
- separate.rs
- deserializer.rs
- roaring.rs
- run_length.rs
- serializer.rs
- async_slice_queue.rs
- bundles.rs
- colors_manager.rs
- colors_memmap_writer.rs
- lib.rs
- managers.rs
- non_colored.rs
- parsers.rs
- storage.rs
- Cargo.toml
- lib.rs
- Cargo.toml
- dumper_colormap_querying.rs
- dumper_colormap_reading.rs
- dumper_minimizer_bucketing.rs
- lib.rs
- pipeline.rs
- Cargo.toml
- hashes-bench.rs
- cn_rkhash_base.rs
- cn_seqhash_base.rs
- fw_rkhash_base.rs
- fw_seqhash_base.rs
- batch_minqueue.rs
- minqueue_testing.rs
- cn_nthash.rs
- cn_rkhash.rs
- cn_seqhash.rs
- dummy_hasher.rs
- extremal.rs
- fw_rkhash.rs
- fw_seqhash.rs
- lib.rs
- nthash_base.rs
- rolling.rs
- Cargo.toml
- creads_utils.rs
- extra_data.rs
- temp_reads.rs
- memvarint.rs
- fasta.rs
- general.rs
- hash_entry.rs
- unitig_link.rs
- compressed_read.rs
- concurrent.rs
- concurrent_filewriter.rs
- ident_writer.rs
- lib.rs
- lines_reader.rs
- memstorage.rs
- partial_unitigs_extra_data.rs
- sequences_reader.rs
- sequences_stream.rs
- structs.rs
- varint.rs
- Cargo.toml
- debug_bucket_stats.rs
- lib.rs
- processor.rs
- resplitter.rs
- Cargo.toml
- macros.rs
- lib.rs
- stats.rs
- Cargo.toml
- compactor.rs
- decode_helper.rs
- lib.rs
- queue_data.rs
- reader.rs
- resplit_bucket.rs
- sequences_splitter.rs
- split_buckets.rs
- Cargo.toml
- colored_query_output.rs
- colormap_reading.rs
- counters_sorting.rs
- parallel_kmers_query.rs
- querier_minimizer_bucketing.rs
- query_colored_counters.rs
- lib.rs
- pipeline.rs
- structs.rs
- Cargo.toml
- binary.rs
- concurrent.rs
- fasta.rs
- gfa.rs
- stream_finish.rs
- indirect_reads_extractor.rs
- lib.rs
- sequences_joiner.rs
- structured_sequences.rs
- Cargo.toml
- lib.rs
- map_entry.rs
- Cargo.toml
- assembler_phases.rs
- debug_functions.rs
- fast_rand_bool.rs
- fuzzy_buckets.rs
- fuzzy_hashmap.rs
- inline_vec.rs
- lib.rs
- owned_drop.rs
- resize_containers.rs
- resource_counter.rs
- vec_slice.rs
- Cargo.toml
- query.fa
- sal1.fa
- sal2.fa
- sal3.fa
- dynamic-dispatch-rs
- instrumenter-rs
- mt-debug-counters-rs
- nightly-quirks-rs
- papi-bindings-rs
- parallel-processor-rs
- streaming-libdeflate-rs
- build_checking.sh
- .gitignore
- .gitmodules
- Cargo.lock
- Cargo.toml
- LICENSE
- README.md
- rust-toolchain
# Installation Guide
1. Get the code
git clone https://github.com/algbio/ggcat
Downloads the entire project code from GitHub to your computer.
cd ggcat
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Rust (rustup) Rust is required to use cargo.
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
Downloads and runs the official install script in one line β this handles the full setup automatically.
cargo install --path crates/cmdline/ --locked
Type this command into your terminal and run it.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Rust
MediumPrerequisites
- Git Needed to download the project code from GitHub.
- Rust (rustup) Installing via rustup also installs cargo.
cargo install --path crates/cmdline/ --locked
Type this command into your terminal and run it.
If cargo build finishes without errors, it worked. The executable is created under target/.
Pulled directly from this repo's README.
4. Make
MediumPrerequisites
- Git Needed to download the project code from GitHub.
- Make Usually pre-installed on Linux/macOS. On Windows, install separately (e.g. via MSYS2 or WSL).
β οΈ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.
cd crates/capi/ggcat-cpp-api
This project's files live in a subfolder, so move into it first.
make
Compiles the code based on the generated build configuration to produce an executable.
If it finishes without errors, it worked. Try running the generated executable directly.
// repository documentation
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