{"id":16713107,"url":"https://github.com/adamtaranto/reconcile","last_synced_at":"2025-03-15T05:18:40.084Z","repository":{"id":73743439,"uuid":"84683779","full_name":"Adamtaranto/RECONcile","owner":"Adamtaranto","description":"Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus 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RECONcile\n\n# Table of contents\n\n* [About RECONcile](#about-reconcile)\n* [Options and usage](#options-and-usage)\n    * [Installing RECONcile](#installing-reconcile)\n    * [Example Workflow](#example-workflow)\n    * [Standard options](#standard-options)\n* [License](#license)\n\n# About RECONcile\n\nTake clustered element fragment coordinates from RECON and write sequences to FASTA for alignment and consensus calling.\n\n# Options and usage\n\n## Installing RECONcile\n\nInstall from this repository.\n\n```bash\ngit clone https://github.com/Adamtaranto/RECONcile.git \u0026\u0026 cd RECONcile\n```\n\n## Example Workflow\n\n**Get total count and names of candidate TEs for RECON**  \n\n```bash\nawk '/^\u003e/ {print $1;} ' Unclustered_candidate_TEs.fa | wc -l | sed 's/^ *//g' \u003e denovo_names.txt  \nawk '/^\u003e/ {print $1;} ' Unclustered_candidate_TEs.fa | sed 's/\u003e//g' | sed 's/^ *//g' \u003e\u003e temp_names.txt  \n```\n\n**Sort in lexical order**\n\n```bash\ncat temp_names.txt | sort \u003e\u003e denovo_names.txt  \nrm temp_names.txt  \n```\n\n**Run All vs All BLAST**  \n\n```bash\nblastn -subject Unclustered_candidate_TEs.fa -query Unclustered_candidate_TEs.fa \\  \n-out denovo_all_v_all.tab -evalue 0.001 -outfmt 6 -task blastn -max_target_seqs 1000  \n```\n\n**Keep all non-self hits with bitscore \u003e 100**  \n\n```bash\nawk '{if ($1 != $2 \u0026\u0026 $12 \u003e= 100) print;}' denovo_all_v_all.tab \u003e filtered_hits.tab  \n```\n\n**MSPCollect fails, use [blast2MSP.pl](https://gist.github.com/sestaton/ea770a26032983e49189#file-blast2msp-pl) to convert to blast result to MSP format instead:**  \n\n```bash\n./blast2MSP.pl filtered_hits.tab \u003e MSP_denovo.out  \n```\n\n**Run RECON**  \n\n```bash\n./RECON-1.08/scripts/recon.pl denovo_names.txt MSP_denovo.out 1  \n```\n\n**Clean up eles output file from RECON**  \n\n```bash\nawk '!/^#/ {print;}' eles | sed 's/\\( \\)*/\\1/g' | cut -d' ' -f 2- \u003e Clean_Eles.txt  \n```\n\n**Fetch fragments for each family**  \n\n```bash\n./RECON_cluster.py -i Unclustered_candidate_TEs.fa -e Clean_Eles.txt -d output_clusters  \n```  \n\n**Align clustered fragments with MAFFT**  \n\n```bash\nmkdir mafftaligns  \nfor i in $(find output_clusters -name '*.fa' | sort);do  \nbase=$(basename $i)  \nname=\"${base%.*}\"  \nmafft $i \u003e 'mafftaligns/'$name'.aln'  \ndone  \n```\n\n**Build concensus sequences from alignments with [cons](http://www.bioinformatics.nl/cgi-bin/emboss/help/cons)**  \n\n```bash\nmkdir consensus_fasta  \nfor i in $(find mafftaligns -name '*.aln' | sort);do  \nbase=$(basename $i)  \nname=\"${base%.*}\"  \ncons -sequence $i -identity 0 -snucleotide1 -supper1 -name $name'_consensus' \\  \n-outseq 'consensus_fasta2/'$name'_consensus.fa' -auto  \ndone  \n```\n\n**Concatenate all consensus sequences and convert to uppercase**  \n\n```bash\nrm RECON_consensus.fa  \ntouch RECON_consensus.fa  \nfor x in $(find consensus_fasta -name '*.fa' | sort);do  \ntr [:lower:] [:upper:] \u003c $x \u003e\u003e RECON_consensus.fa  \ndone  \n``` \n\n## Standard options\n\n```bash\nUsage: RECONcile [-h] -i INFASTA [-e ELES] [-d OUTDIR]\n\nExtracts and orients TE frags belonging to RECON clusters.\n\nOptional arguments:\n  -h, --help        Show this help message and exit\n  -i, --inFasta     Multi fasta containing all TE sequences.\n  -e, --eles        Space delimited 'ele' file from RECON.\n  -d, --outDir      Directory for new cluster files to be written to.\n```\n\n# License\n\nSoftware provided under MIT license.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadamtaranto%2Freconcile","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadamtaranto%2Freconcile","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadamtaranto%2Freconcile/lists"}