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1. tblastn_exon_stitcher tblastn_exon_stitcher Public

   Need an ORF from an unannotated genome? This script exploits ncbi's ability to tBLASTn against genome assemblies, to get provisional exon sets from BLAST query-hit alignments.

   Jupyter Notebook

2. condense_InterProScan_annots condense_InterProScan_annots Public

   InterProScan is useful, but its annots are multiline and redundant. This collapses them into a single, human-readable line for each annotated sequence.

   Python

3. Protein_renamer Protein_renamer Public

   Tools to add phylogeny-ready names (including accession, genus, species, lineage & taxid) to protein fastas from any of (A) genbank (B) SRA (C) Genome_paper_supp_data

   Python

4. HGT_v_Contamination_assessor HGT_v_Contamination_assessor Public

   How can we discriminate contaminants from HGT? Alien indices are often used to screen out foreign sequences, but can 'overclean' by removing bona fide HGT. This script leverages metadata about each…

   Python

5. infer_splice_variants_from_Trinity infer_splice_variants_from_Trinity Public

   Did you know that Trinity predicts splice variants? (Chrysalis works even for de novo transcriptomes, and its input--though heuristic--is valuable). Likewise, TransDecoder can predict multiple ORFs…

   Python

6. automated_phylogenies automated_phylogenies Public

   Nextflow