hinge_0.5.0-3_amd64.deb


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Description

hinge - long read genome assembler based on hinging

Property Value
Distribution Ubuntu 18.04 (Bionic Beaver)
Repository Ubuntu Universe amd64
Package name hinge
Package version 0.5.0
Package release 3
Package architecture amd64
Package type deb
Installed size 2.39 KB
Download size 382.04 KB
Official Mirror archive.ubuntu.com
HINGE is a genome assembler that seeks to achieve optimal repeat resolution
by distinguishing repeats that can be resolved given the data from those that
cannot. This is accomplished by adding “hinges” to reads for constructing an
overlap graph where only unresolvable repeats are merged. As a result, HINGE
combines the error resilience of overlap-based assemblers with
repeat-resolution capabilities of de Bruijn graph assemblers.

Alternatives

Package Version Architecture Repository
hinge - - -

Requires

Name Value
daligner -
dascrubber -
dazzdb -
libc6 >= 2.14
libgcc1 >= 1:3.0
libgomp1 >= 4.2.1
libstdc++6 >= 5.2
python -
python-colormap -
python-configparser -
python-matplotlib -
python-networkx -
python-numpy -
python-pbcore -
python-ujson -
zlib1g >= 1:1.1.4

Download

Type URL
Binary Package hinge_0.5.0-3_amd64.deb
Source Package hinge

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install hinge deb package:
    # sudo apt-get install hinge

Files

Path
/usr/bin/hinge
/usr/lib/hinge/Reads_filter
/usr/lib/hinge/Visualise_graph.py
/usr/lib/hinge/add_groundtruth.py
/usr/lib/hinge/add_groundtruth_json.py
/usr/lib/hinge/clip_ends.py
/usr/lib/hinge/compute_n50_from_draft.py
/usr/lib/hinge/condense_graph.py
/usr/lib/hinge/condense_graph_and_annotate.py
/usr/lib/hinge/condense_graph_annotate_clip_ends.py
/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py
/usr/lib/hinge/condense_graph_with_gt.py
/usr/lib/hinge/connected.py
/usr/lib/hinge/consensus
/usr/lib/hinge/correct_head.py
/usr/lib/hinge/create_bandage_file.py
/usr/lib/hinge/create_hgraph.py
/usr/lib/hinge/create_hgraph_nogt.py
/usr/lib/hinge/download_NCTC_pipeline.py
/usr/lib/hinge/draft_assembly
/usr/lib/hinge/draft_assembly.py
/usr/lib/hinge/draft_assembly_not_perfect.py
/usr/lib/hinge/draw2.py
/usr/lib/hinge/draw2_pileup.py
/usr/lib/hinge/draw2_pileup_region.py
/usr/lib/hinge/draw2_pileup_w_repeat.py
/usr/lib/hinge/draw_pileup_region.py
/usr/lib/hinge/draw_pileup_region_find_bridges.py
/usr/lib/hinge/fasta_to_fastq.py
/usr/lib/hinge/get_NCTC_json.py
/usr/lib/hinge/get_consensus_gfa.py
/usr/lib/hinge/get_draft_annotation.py
/usr/lib/hinge/get_draft_path.py
/usr/lib/hinge/get_draft_path_norevcomp.py
/usr/lib/hinge/get_maximal_reads
/usr/lib/hinge/get_single_strand.py
/usr/lib/hinge/hinging
/usr/lib/hinge/interface_utils.py
/usr/lib/hinge/longest_path.py
/usr/lib/hinge/merge_hinges.py
/usr/lib/hinge/parallel_draw.sh
/usr/lib/hinge/parallel_draw_large.sh
/usr/lib/hinge/parse.py
/usr/lib/hinge/parse_alignment.py
/usr/lib/hinge/parse_qv.py
/usr/lib/hinge/parse_read.py
/usr/lib/hinge/pileup.ipynb
/usr/lib/hinge/pipeline_consensus.py
/usr/lib/hinge/pipeline_consensus_norevcomp.py
/usr/lib/hinge/pipeline_nctc.py
/usr/lib/hinge/pruning_and_clipping.py
/usr/lib/hinge/pruning_and_clipping_nanopore.py
/usr/lib/hinge/random_condensation.py
/usr/lib/hinge/repeat_annotate_reads.py
/usr/lib/hinge/run_mapping.py
/usr/lib/hinge/run_mapping2.py
/usr/lib/hinge/run_mapping3.py
/usr/lib/hinge/run_parse_alignment.py
/usr/lib/hinge/run_parse_read.py
/usr/lib/hinge/split_las.py
/usr/lib/hinge/unitig.py
/usr/share/doc/hinge/README.md.gz
/usr/share/doc/hinge/changelog.Debian.gz
/usr/share/doc/hinge/copyright
/usr/share/doc/hinge/parameter_description.md.gz
/usr/share/doc/hinge/examples/demo/NCTC9657_demo/run.sh
/usr/share/doc/hinge/examples/demo/ecoli_P4_demo/run.sh
/usr/share/doc/hinge/examples/demo/ecoli_demo/run.sh
/usr/share/doc/hinge/examples/demo/ecoli_demo/run_norevcomp.sh
/usr/share/doc/hinge/examples/demo/ecoli_nanopore/run.sh
/usr/share/doc/hinge/examples/demo/yeast_W303_demo/nominal.ini
/usr/share/doc/hinge/examples/demo/yeast_W303_demo/run.sh
/usr/share/doc/hinge/examples/utils/nominal.ini
/usr/share/man/man1/hinge.1.gz

Changelog

2018-02-04 - Afif Elghraoui <afif@debian.org>
hinge (0.5.0-3) unstable; urgency=low
* Mark spdlog patch as forwarded upstream
* d/control: copy Depends into Build-Depends
to allow migration to Testing
* Bump Standards-Version to 4.1.3
* Bump copyright year
2017-12-13 - Gert Wollny <gewo@debian.org>
hinge (0.5.0-2) unstable; urgency=medium
* Team upload.
* d/p/libspdlog: Update to new interface, Closes: #884211
* d/control: Update to standards 4.1.1 (no changes needed)
2017-10-20 - Afif Elghraoui <afif@debian.org>
hinge (0.5.0-1) unstable; urgency=medium
* Initial release (Closes: #878962)

See Also

Package Description
hippomocks_5.0-1_amd64.deb C++ mocking framework
hisat2_2.1.0-1_amd64.deb graph-based alignment of short nucleotide reads to many genomes
hitch_1.4.4-1build1_amd64.deb scalable TLS proxy
hitori_3.22.4-1_amd64.deb logic puzzle game similar to sudoku
hledger-interest_1.5.1-1_amd64.deb interest computing for (h)ledger
hledger-ui_1.2-1_amd64.deb curses-style user interface for the hledger accounting tool
hledger-web_1.2-1_amd64.deb web interface for the hledger accounting tool
hledger_1.2-1build3_amd64.deb command-line double-entry accounting program
hlins_0.39-23_all.deb Insert URLs into html documents
hlint_2.0.11-1build1_amd64.deb Haskell source code suggestions
hmmer-doc_3.1b2+dfsg-5ubuntu1_all.deb profile hidden Markov models for protein sequence analysis (docs)
hmmer-examples_3.1b2+dfsg-5ubuntu1_all.deb profile hidden Markov models for protein sequence analysis (examples)
hmmer2-doc_2.3.2+dfsg-5_all.deb profile hidden Markov models for protein sequence analysis (docs)
hmmer2-pvm_2.3.2+dfsg-5_amd64.deb HMMER programs with PVM (Parallel Virtual Machine) support
hmmer2_2.3.2+dfsg-5_amd64.deb profile hidden Markov models for protein sequence analysis
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