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        "description": "abeona\n======\n\n.. image:: https://travis-ci.org/winni2k/abeona.svg?branch=master\n    :alt: Travis-CI Build Status\n    :target: https://travis-ci.org/winni2k/abeona\n\n.. image:: https://img.shields.io/github/commits-since/winni2k/abeona/v0.45.0.svg\n    :alt: Commits since latest release\n    :target: https://github.com/winni2k/abeona/compare/v0.45.0...master\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat\n    :alt: freedom\n    :target: http://bioconda.github.io/recipes/abeona/README.html\n\nabeona v0.45.0\n\nA simple transcriptome assembler based on kallisto and Cortex graphs.\n\nAbeona consists of the following stages:\n\n1. Assembly of reads into a De Bruijn graph\n2. Pruning of tips and low-coverage unitigs\n3. Partitioning of the De Bruijn graph into subgraphs\n4. Generation of candidate transcripts by simple path traversal\n5. Filtering of candidate transcripts by kallisto\n\nInstallation\n------------\n\nThe easiest way to install abeona is into a `conda <https://conda.io/miniconda.html>`_ environment.\n\nAfter activating the conda environment, run:\n\n.. code-block:: bash\n\n    conda install abeona -c conda-forge -c bioconda\n\nUsage\n-----\n\nThe principal command is ``abeona assemble``. This command assembles transcripts from cleaned\nshort-read RNA-seq reads in FASTA or FASTQ format. A description of command arguments is\navailable with the command:\n\n.. code-block:: bash\n\n    abeona assemble --help\n\nSpecifying input read data\n~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nAbeona is designed to be run on reads from one biological sample at a time.\nAbeona uses sequencing reads in two stages: for De Bruijn-graph construction,\nand for candidate transcript filtering with kallisto. The first stage accepts\npaired-end, single-end, or both types of reads through the ``--fastx-*`` arguments.\nThe reads for the second stage are specified with the ``--kallisto-fastx-*`` arguments.\nKallisto only accepts single-end or paired-end reads, so input to this stage\nis also restricted in that manner.\n\nToy Example\n-----------\n\n.. code-block:: bash\n\n    # Let's create a FASTA consisting of sub-reads from two transcripts: AAAAACCC and AAAAAGGG\n    $ for s in AAAAACC AAAAAGG AAAACCC AAAAGGG; do for i in $(seq 1 3); do echo -e \">_\\n$s\" >> input.fa; done; done\n\n    # Now feed the fasta to the graph assembly step with --fastx-single and to the kallisto filtering\n    # step with --kallisto-fastx-single.\n    $ abeona assemble -k 5 -m 4 --fastx-single input.fa --kallisto-fastx-single \\\n        input.fa --kallisto-fragment-length 7 --kallisto-sd 1 -o test --no-links\n    N E X T F L O W  ~  version 0.31.1\n    Launching `assemble.nf` [determined_allen] - revision: 11c20ed355\n    [bootstrap_samples:100, fastx_forward:null, fastx_reverse:null, fastx_single:/Users/winni/tmp/input.fa, initial_contigs:null, jobs:2, kallisto_fastx_forward:null, kallisto_fastx_reverse:null, kallisto_fastx_single:/Users/winni/tmp/input.fa, kallisto_fragment_length:7.0, kallisto_sd:1.0, kmer_size:5, max_paths_per_subgraph:0, memory:4, merge_candidates_before_kallisto:false, min_tip_length:0, min_unitig_coverage:4, out_dir:test, quiet:false, resume:false, mccortex:mccortex 5, mccortex_args:--sort --force -m 4G]\n    [warm up] executor > local\n    [26/119d41] Submitted process > fullCortexGraph\n    [fc/585605] Submitted process > cleanCortexGraph\n    [dd/40b5fc] Submitted process > pruneCortexGraphOfTips\n    [36/f63343] Submitted process > traverseCortexSubgraphs\n    [23/6d9033] Submitted process > candidateTranscripts (1)\n    [d5/05d417] Submitted process > buildKallistoIndices (1)\n    [ac/e36d53] Submitted process > kallistoQuant (1)\n    [ec/2b258d] Submitted process > filter_transcripts (1)\n    [49/d4c7e3] Submitted process > concatTranscripts\n\n    # View the resulting assembled transcripts\n    $ zcat test/all_transcripts/transcripts.fa.gz\n    >g0_p0 prop_bs_est_counts_ge_1=0.98\n    AAAAAGGG\n    >g0_p1 prop_bs_est_counts_ge_1=1.0\n    AAAAACCC\n\nDevelopment\n-----------\n\n::\n\n    conda env create -f environment.yml my-dev-env\n    conda activate my-dev-env\n    make test\n\nLicense\n-------\n\nAbeona is distributed under the terms of the\n`Apache License, Version 2.0 <https://choosealicense.com/licenses/apache-2.0>`_.\n\nCiting\n------\n\nIf you use abeona in your research, please cite:\n\n    Akhter S, Kretzschmar WW, Nordal V, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundstr\u00f6m JF. Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies. Front. Plant Sci. 9, 1\u201318 (2018).\n\nChangelog\n---------\n\nVersion 0.45.0\n~~~~~~~~~~~~~~\n\n:Date: XXX\n\nNew features\n............\n\n**abeona assemble**\n\n* Mccortex is now used for pruning by default\n* The command line argument ``--prune-tips-with-mccortex`` is now deprecated.\n  Instead use ``--no-prune-tips-with-mccortex``.\n* New iterative pruning strategy ``--prune-tips-iteratively``.\n\nVersion 0.44.0\n~~~~~~~~~~~~~~\n\n:Date: 2019-03-26\n\nThis version skips commits made for the 0.43.0 tag.\n\nNew features\n............\n\n* Reads that share kmers with subgraphs that are skipped are now reported in the\n  ``unassembled_reads`` directory.\n\nVersion 0.42.0\n~~~~~~~~~~~~~~\n\n:Date: 2018-12-17\n\nInterface Changes\n.................\n\n* Cleanup now deletes all directories in output dir except for ``all_transcripts/transcripts.fa.gz``\n* Cleanup is now on by default\n* Cleanup can be turned off with ``--no-cleanup`` flag\n* ``all_transcripts/transcripts.fa.gz`` is unzipped and stored as ``transcripts.fa`` to conform\n  to the convention set by Trinity and Oases for output file names\n\nVersion 0.41.0\n~~~~~~~~~~~~~~\n\n:Date: 2018-12-13\n\nInterface changes\n.................\n\n* Remove ``--kallisto-fastx-*`` arguments. Being able to separately specify reads to graph building\n  and kallisto has not been all that useful, and it increases the complexity of the code.\n* Add default value of ``--kmer-size`` for ``--min-tip-length``.\n\nFixes\n.....\n\n* There are several ways in which kallisto can fail due to no reads pseudoaligning to a subgraph's\n  candidate transcripts. When this happens, abeona now catches the error and silently ignores the\n  subgraph.\n\n\nVersion 0.40.0\n~~~~~~~~~~~~~~\n\n:Date: 2018-11-17\n\nNew features\n............\n\n* Add ``--no-links`` argument to turn off link use in candidate transcript creation\n* Add ``--max-junctions`` argument to allow fast skipping of subgraphs with too many junctions\n\nFixes\n.....\n\n* Properly assign reads to all subgraphs to which they are assignable\n* Solve high-mem use problem by creating links only on assigned reads\n\nVersion 0.36.0\n~~~~~~~~~~~~~~\n\n:Date: 2018-10-25\n\nNew features\n............\n\n* Graph traversal now uses links\n\nFixes\n.....\n\n* Lots of improvements to ``abeona reads`` to improve memory and filehandle use\n\nVersion 0.33.0\n~~~~~~~~~~~~~~\n\n:Date: 2018-10-17\n\nNew features\n............\n\n* Use kmer mapping (``abeona reads``) to assign reads to subgraphs before quantification of\n  candidate transcripts with kallisto\n\nFixes\n.....\n\n* Add missing conda dependency ``seqtk`` to ``environment.yml`` for travis CI\n\n\n",
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