abeona

abeona

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abeona v0.45.0

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

Development
-----------

::

    conda env create -f environment.yml my-dev-env
    conda activate my-dev-env
    make test

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 0.45.0
~~~~~~~~~~~~~~

:Date: XXX

New features
............

**abeona assemble**

* Mccortex is now used for pruning by default
* The command line argument ``--prune-tips-with-mccortex`` is now deprecated.
  Instead use ``--no-prune-tips-with-mccortex``.
* New iterative pruning strategy ``--prune-tips-iteratively``.

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