Package: abeona
abeona v0.45.0A simple transcriptome assembler based on kallisto and Cortex graphs.Abeona consists of the following stages:Assembly of reads into a De Bruijn graphPruning of tips and low-coverage unitigsPartitioning of the De Bruijn graph into subgraphsGeneration of candidate transcripts by simple path traversalFiltering of candidate transcripts by kallistoInstallationThe easiest way to install abeona is into acondaenvironment.After activating the conda environment, run:condainstallabeona-cconda-forge-cbiocondaUsageThe principal command isabeona 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:abeonaassemble--helpSpecifying input read dataAbeona 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$forsinAAAAACCAAAAAGGAAAACCCAAAAGGG;doforiin$(seq13);doecho-e">_\n$s">>input.fa;done;done# Now feed the fasta to the graph assembly step with --fastx-single and to the kallisto filtering
# step with --kallisto-fastx-single.$abeonaassemble-k5-m4--fastx-singleinput.fa--kallisto-fastx-single\input.fa--kallisto-fragment-length7--kallisto-sd1-otest--no-linksNEXTFLOW~version0.31.1Launching`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:mccortex5,mccortex_args:--sort--force-m4G][warmup]executor>local[26/119d41]Submittedprocess>fullCortexGraph[fc/585605]Submittedprocess>cleanCortexGraph[dd/40b5fc]Submittedprocess>pruneCortexGraphOfTips[36/f63343]Submittedprocess>traverseCortexSubgraphs[23/6d9033]Submittedprocess>candidateTranscripts(1)[d5/05d417]Submittedprocess>buildKallistoIndices(1)[ac/e36d53]Submittedprocess>kallistoQuant(1)[ec/2b258d]Submittedprocess>filter_transcripts(1)[49/d4c7e3]Submittedprocess>concatTranscripts# View the resulting assembled transcripts$zcattest/all_transcripts/transcripts.fa.gz>g0_p0prop_bs_est_counts_ge_1=0.98AAAAAGGG>g0_p1prop_bs_est_counts_ge_1=1.0AAAAACCCDevelopmentconda env create -f environment.yml my-dev-env
conda activate my-dev-env
make testLicenseAbeona is distributed under the terms of theApache License, Version 2.0.CitingIf 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).ChangelogVersion 0.45.0Date:XXXNew featuresabeona assembleMccortex is now used for pruning by defaultThe command line argument--prune-tips-with-mccortexis now deprecated.
Instead use--no-prune-tips-with-mccortex.New iterative pruning strategy--prune-tips-iteratively.Version 0.44.0Date:2019-03-26This version skips commits made for the 0.43.0 tag.New featuresReads that share kmers with subgraphs that are skipped are now reported in theunassembled_readsdirectory.Version 0.42.0Date:2018-12-17Interface ChangesCleanup now deletes all directories in output dir except forall_transcripts/transcripts.fa.gzCleanup is now on by defaultCleanup can be turned off with--no-cleanupflagall_transcripts/transcripts.fa.gzis unzipped and stored astranscripts.fato conform
to the convention set by Trinity and Oases for output file namesVersion 0.41.0Date:2018-12-13Interface changesRemove--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.FixesThere 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 0.40.0Date:2018-11-17New featuresAdd--no-linksargument to turn off link use in candidate transcript creationAdd--max-junctionsargument to allow fast skipping of subgraphs with too many junctionsFixesProperly assign reads to all subgraphs to which they are assignableSolve high-mem use problem by creating links only on assigned readsVersion 0.36.0Date:2018-10-25New featuresGraph traversal now uses linksFixesLots of improvements toabeona readsto improve memory and filehandle useVersion 0.33.0Date:2018-10-17New featuresUse kmer mapping (abeona reads) to assign reads to subgraphs before quantification of
candidate transcripts with kallistoFixesAdd missing conda dependencyseqtktoenvironment.ymlfor travis CI