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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.
After activating the conda environment, run:
conda install abeona -c conda-forge -c bioconda
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.
# 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
conda 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).
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.
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_reads directory.
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
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.
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.
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
Properly assign reads to all subgraphs to which they are assignable
Solve high-mem use problem by creating links only on assigned reads
Graph traversal now uses links
Lots of improvements to abeona reads to improve memory and filehandle use
Use kmer mapping (abeona reads) to assign reads to subgraphs before quantification of candidate transcripts with kallisto
Add missing conda dependency seqtk to environment.yml for travis CI
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