abeona 0.45.0

Description:

abeona 0.45.0

abeona v0.45.0
A simple transcriptome assembler based on kallisto and Cortex graphs.
Abeona consists of the following stages:

Assembly of reads into a De Bruijn graph
Pruning of tips and low-coverage unitigs
Partitioning of the De Bruijn graph into subgraphs
Generation of candidate transcripts by simple path traversal
Filtering of candidate transcripts by kallisto


Installation
The easiest way to install abeona is into a conda environment.
After activating the conda environment, run:
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:
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
# 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.


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