Coding & Dev Tools

Create IEP templates for individualized education. TRIGGERS - Use when user needs help with iep-template related tasks.

Design JWT strategies with refresh tokens. TRIGGERS - Use when user needs help with jwt-strategy related tasks.

Write leave policies covering PTO, sick, and family leave. TRIGGERS - Use when user needs help with leave-policy related tasks.

Write op-ed pieces with arguments. TRIGGERS - Use when user needs help with op-ed-writer related tasks.

Design personal CRM systems for networking. TRIGGERS - Use when user needs help with personal-crm related tasks.

Create performance improvement plan templates. TRIGGERS - Use when user needs help with pip-template related tasks.

Design pulse surveys for rapid employee feedback. TRIGGERS - Use when user needs help with pulse-survey related tasks.

Build quizzes with question types and scoring. TRIGGERS - Use when user needs help with quiz-builder related tasks.

Design reading plans with retention strategies. TRIGGERS - Use when user needs help with reading-plan related tasks.

Use when aligning low-divergence DNA sequence reads to a reference genome

Use when converting ViennaRNA-style sequence-plus-dot-bracket records on stdin into RNA connectivity-table output.

Use when working from the local Evo 2 repository for DNA-sequence scoring, embeddings, generation, or phage-genome design experiments.

Use when you need to compress or decompress files using BGZF (Blocked GNU Zip Format), create BGZF indexes for random access, or prepare bioinformatics files for tabix indexing.

Use when converting RNA connectivity-table (`.ct`) files into extended FASTA with dot-bracket structures, optionally removing pseudoknots or modified bases.

Use when invoking the top-level `easel` dispatcher to discover or run Easel sequence-analysis subcommands from the HMMER toolchain.

Use when you need to post unique identifiers or accession numbers to NCBI Entrez databases for subsequent retrieval operations

Use when processing raw FASTQ files for quality control, adapter trimming, length or complexity filtering, polyG tail trimming, or generating QC reports before downstream analysis.

Use when performing multiple sequence alignment on nucleotide or protein sequences, such as preparing alignments for phylogenetic analysis or comparative genomics.

Use when doing lightweight FASTA/FASTQ transformations such as conversion, subsampling, subsequence extraction, trimming, or quick QC with seqtk.

Use when you need to index or query tab-delimited genomic files for fast region-based retrieval.

Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.

Use when comparing protein sequences against protein databases for similarity searches, homology detection, or functional annotation.

Use when you need to fetch records or data from NCBI Entrez databases (PubMed, nucleotide, protein, gene, SRA, etc.) by ID or accession

Use when you need to perform quality control analysis on high-throughput sequencing data (fastq, bam, sam, or fast5 files) to identify potential problems before downstream analysis.

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

Use when performing multiple sequence alignment of FASTA inputs, generating alignment ensembles, or calculating alignment confidence metrics.

Use when searching DNA or RNA queries against nucleotide sequence databases with HMMER's nucleotide homology search engine.

Use when making raw HTTP, E-utilities, PubChem, datasets, or FTP requests through the low-level EDirect transport wrapper.

Use when paired-end reads need to be reordered so mates appear consecutively, or when preparing BAM files for featureCounts by adding dummy reads for singletons.

Use when summarizing an RNA folding landscape by counting how many structures fall into each energy band, rather than enumerating individual folds one by one.

Use when working with FASTA or FASTQ files for statistics, filtering, transformation, format conversion, searching, or set operations.

Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.

Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.

Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.

Use when filtering Entrez search results by date, organism, publication type, sequence features, or other database-specific criteria in bioinformatics pipelines.

Use when filling ancestral alleles into the INFO column of VCF files using ancestral alignment data from 1000 Genomes or similar sources.