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
The easiest way to install abeona is into a conda environment.
To create a conda environment named "abeona" run:
conda install create -n abeona abeona -c conda-forge -c bioconda -y
# activate the environment
conda activate abeonaThe 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 --helpAbeona 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.
# 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
# keep a log in test.log
$ abeona assemble -k 5 -m 4 --fastx-single input.fa --min-tip-length 1 \
--kallisto-fragment-length 7 --kallisto-sd 1 -o test --no-links \
2>&1 | tee test.log
N E X T F L O W ~ version 19.01.0
Launching `assemble.nf` [marvelous_rosalind] - revision: 78bfc98f1f
Running nextflow script for abeona v0.45.0
Nextflow arguments from args.json:
{
"assemble_unassembled_reads_with_transabyss": false,
"bootstrap_proportion_threshold": 0.95,
"bootstrap_samples": 100,
"estimated_count_threshold": 1,
"extra_start_kmer": null,
"fastx_forward": null,
"fastx_reverse": null,
"fastx_single": "/Volumes/mac-3/home/Projects/caina/2020-08-24_abeona/input.fa",
"initial_contigs": null,
"jobs": 2,
"kallisto_fragment_length": 7.0,
"kallisto_sd": 1.0,
"kallisto_threads": 2,
"kmer_size": "5",
"max_junctions": 0,
"max_paths_per_subgraph": 0,
"max_read_length": 7,
"memory": 4,
"min_tip_length": 1,
"min_unitig_coverage": 4,
"no_cleanup": false,
"no_links": true,
"no_prune_tips_with_mccortex": false,
"out_dir": "test",
"prune_tips_iteratively": false,
"prune_tips_with_mccortex": true,
"quiet": false,
"record_buffer_size": -1,
"report_unassembled_reads": false,
"resume": false,
"with_dag": false,
"with_report": false,
"mccortex": "mccortex 5",
"mccortex_args": "--sort --force -m 4G",
"mccortex_thread_args": "--force -m 2G"
}
[warm up] executor > local
[3d/255de7] Submitted process > fullCortexGraph
[2c/c20fdf] Submitted process > cleanCortexGraph
[b0/909834] Submitted process > traverseCortexSubgraphs (1)
[b2/c75eec] Submitted process > createSubgraphList
[18/2c45c7] Submitted process > assignReadsToSubgraphs
[f8/b4c61b] Submitted process > threadReads (1)
[d9/7e6528] Submitted process > candidateTranscripts (1)
[25/ed539b] Submitted process > buildKallistoIndices (1)
[c7/9c5b50] Submitted process > kallistoQuant (1)
[e7/5b2330] Submitted process > filter_transcripts (1)
[9d/3f9fa5] Submitted process > concatTranscripts
# View the resulting assembled transcripts
$ cat test/transcripts.fa
>g0_p0 prop_bs_est_counts_ge_1=0.99;est_count=3
AAAAAGGG
>g0_p1 prop_bs_est_counts_ge_1=0.97;est_count=3
AAAAACCCconda env create -f environment.yml my-dev-env conda activate my-dev-env make test
Abeona is distributed under the terms of the Apache License, Version 2.0.
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).
| Date: | XXX |
|---|
abeona assemble
- Mccortex is now used for pruning by default
- The command line argument
--prune-tips-with-mccortexis now deprecated. Instead use--no-prune-tips-with-mccortex. - New iterative pruning strategy
--prune-tips-iteratively.
| Date: | 2019-03-26 |
|---|
This version skips commits made for the 0.43.0 tag.
- Reads that share kmers with subgraphs that are skipped are now reported in the
unassembled_readsdirectory.
| Date: | 2018-12-17 |
|---|
- 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-cleanupflag all_transcripts/transcripts.fa.gzis unzipped and stored astranscripts.fato conform to the convention set by Trinity and Oases for output file names
| Date: | 2018-12-13 |
|---|
- 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-sizefor--min-tip-length.
- 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.
| Date: | 2018-11-17 |
|---|
- Add
--no-linksargument to turn off link use in candidate transcript creation - Add
--max-junctionsargument to allow fast skipping of subgraphs with too many junctions
- Properly assign reads to all subgraphs to which they are assignable
- Solve high-mem use problem by creating links only on assigned reads
| Date: | 2018-10-25 |
|---|
- Graph traversal now uses links
- Lots of improvements to
abeona readsto improve memory and filehandle use
| Date: | 2018-10-17 |
|---|
- Use kmer mapping (
abeona reads) to assign reads to subgraphs before quantification of candidate transcripts with kallisto
- Add missing conda dependency
seqtktoenvironment.ymlfor travis CI