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abeona
======

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* - tests
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.. |travis| image:: https://travis-ci.org/winni2k/abeona.svg?branch=master
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:alt: Commits since latest release
:target: https://github.com/winni2k/abeona/compare/v0.42.0...master


abeona v0.42.0

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

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 0.42.0
~~~~~~~~~~~~~~

: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


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