Metadata-Version: 1.2
Name: abeona
Version: 0.44.1
Summary: UNKNOWN
Home-page: https://github.com/winni2k/abeona
Author: Warren W. Kretzschmar
Author-email: warrenk@kth.se
Maintainer: Warren W. Kretzschmar
Maintainer-email: warrenk@kth.se
License: Apache-2.0
Description: abeona
        ======
        
        .. image:: https://travis-ci.org/winni2k/abeona.svg?branch=master
            :alt: Travis-CI Build Status
            :target: https://travis-ci.org/winni2k/abeona
        
        .. image:: https://img.shields.io/github/commits-since/winni2k/abeona/v0.44.1.svg
            :alt: Commits since latest release
            :target: https://github.com/winni2k/abeona/compare/v0.44.1...master
        
        .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
            :alt: freedom
            :target: http://bioconda.github.io/recipes/abeona/README.html
        
        abeona v0.44.1
        
        A simple transcriptome assembler based on kallisto and Cortex graphs.
        
        Abeona consists of the following stages:
        
        1. Assembly of reads into a De Bruijn graph
        2. Pruning of tips and low-coverage unitigs
        3. Partitioning of the De Bruijn graph into subgraphs
        4. Generation of candidate transcripts by simple path traversal
        5. Filtering of candidate transcripts by kallisto
        
        Installation
        ------------
        
        The easiest way to install abeona is into a `conda <https://conda.io/miniconda.html>`_ environment.
        
        After activating the conda environment, run:
        
        .. code-block:: bash
        
            conda install abeona -c conda-forge -c bioconda
        
        Usage
        -----
        
        The principal command is ``abeona assemble``. This command assembles transcripts from cleaned
        short-read RNA-seq reads in FASTA or FASTQ format. A description of command arguments is
        available with the command:
        
        .. code-block:: bash
        
            abeona assemble --help
        
        Specifying input read data
        ~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Abeona is designed to be run on reads from one biological sample at a time.
        Abeona uses sequencing reads in two stages: for De Bruijn-graph construction,
        and for candidate transcript filtering with kallisto. The first stage accepts
        paired-end, single-end, or both types of reads through the ``--fastx-*`` arguments.
        The reads for the second stage are specified with the ``--kallisto-fastx-*`` arguments.
        Kallisto only accepts single-end or paired-end reads, so input to this stage
        is also restricted in that manner.
        
        Toy Example
        -----------
        
        .. code-block:: bash
        
            # Let's create a FASTA consisting of sub-reads from two transcripts: AAAAACCC and AAAAAGGG
            $ for s in AAAAACC AAAAAGG AAAACCC AAAAGGG; do for i in $(seq 1 3); do echo -e ">_\n$s" >> input.fa; done; done
        
            # Now feed the fasta to the graph assembly step with --fastx-single and to the kallisto filtering
            # step with --kallisto-fastx-single.
            $ abeona assemble -k 5 -m 4 --fastx-single input.fa --kallisto-fastx-single \
                input.fa --kallisto-fragment-length 7 --kallisto-sd 1 -o test --no-links
            N E X T F L O W  ~  version 0.31.1
            Launching `assemble.nf` [determined_allen] - revision: 11c20ed355
            [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]
            [warm up] executor > local
            [26/119d41] Submitted process > fullCortexGraph
            [fc/585605] Submitted process > cleanCortexGraph
            [dd/40b5fc] Submitted process > pruneCortexGraphOfTips
            [36/f63343] Submitted process > traverseCortexSubgraphs
            [23/6d9033] Submitted process > candidateTranscripts (1)
            [d5/05d417] Submitted process > buildKallistoIndices (1)
            [ac/e36d53] Submitted process > kallistoQuant (1)
            [ec/2b258d] Submitted process > filter_transcripts (1)
            [49/d4c7e3] Submitted process > concatTranscripts
        
            # View the resulting assembled transcripts
            $ zcat test/all_transcripts/transcripts.fa.gz
            >g0_p0 prop_bs_est_counts_ge_1=0.98
            AAAAAGGG
            >g0_p1 prop_bs_est_counts_ge_1=1.0
            AAAAACCC
        
        License
        -------
        
        Abeona is distributed under the terms of the
        `Apache License, Version 2.0 <https://choosealicense.com/licenses/apache-2.0>`_.
        
        Citing
        ------
        
        If you use abeona in your research, please cite:
        
            Akhter S, Kretzschmar WW, Nordal V, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundström 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, 1–18 (2018).``
        
        Changelog
        ---------
        
        Version 0.44.0
        ~~~~~~~~~~~~~~
        
        :Date: 2019-03-26
        
        This version skips commits made for the 0.43.0 tag.
        
        New features
        ............
        
        * Reads that share kmers with subgraphs that are skipped are now reported in the
          ``unassembled_reads`` directory.
        
        Version 0.42.0
        ~~~~~~~~~~~~~~
        
        :Date: 2018-12-17
        
        Interface Changes
        .................
        
        * Cleanup now deletes all directories in output dir except for ``all_transcripts/transcripts.fa.gz``
        * Cleanup is now on by default
        * Cleanup can be turned off with ``--no-cleanup`` flag
        * ``all_transcripts/transcripts.fa.gz`` is unzipped and stored as ``transcripts.fa`` to conform
          to the convention set by Trinity and Oases for output file names
        
        Version 0.41.0
        ~~~~~~~~~~~~~~
        
        :Date: 2018-12-13
        
        Interface changes
        .................
        
        * Remove ``--kallisto-fastx-*`` arguments. Being able to separately specify reads to graph building
          and kallisto has not been all that useful, and it increases the complexity of the code.
        * Add default value of ``--kmer-size`` for ``--min-tip-length``.
        
        Fixes
        .....
        
        * There are several ways in which kallisto can fail due to no reads pseudoaligning to a subgraph's
          candidate transcripts. When this happens, abeona now catches the error and silently ignores the
          subgraph.
        
        
        Version 0.40.0
        ~~~~~~~~~~~~~~
        
        :Date: 2018-11-17
        
        New features
        ............
        
        * Add ``--no-links`` argument to turn off link use in candidate transcript creation
        * Add ``--max-junctions`` argument to allow fast skipping of subgraphs with too many junctions
        
        Fixes
        .....
        
        * Properly assign reads to all subgraphs to which they are assignable
        * Solve high-mem use problem by creating links only on assigned reads
        
        Version 0.36.0
        ~~~~~~~~~~~~~~
        
        :Date: 2018-10-25
        
        New features
        ............
        
        * Graph traversal now uses links
        
        Fixes
        .....
        
        * Lots of improvements to ``abeona reads`` to improve memory and filehandle use
        
        Version 0.33.0
        ~~~~~~~~~~~~~~
        
        :Date: 2018-10-17
        
        New features
        ............
        
        * Use kmer mapping (``abeona reads``) to assign reads to subgraphs before quantification of
          candidate transcripts with kallisto
        
        Fixes
        .....
        
        * Add missing conda dependency ``seqtk`` to ``environment.yml`` for travis CI
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
