Use when you need to extract reference sequences, names, or summary information from a Bowtie2 index file.
EnglishUse when unioning multiple Entrez or NCBI UID files into one deduplicated numeric-sorted list.
EnglishUse when converting RNA connectivity-table (.ct) files into extended FASTA with dot-bracket structures, optionally removing pseudoknots or modified bases.
EnglishUse when auditing or reusing the shared EDirect shell functions that other Entrez Direct wrapper scripts source internally.
EnglishUse when you need to discover available NCBI Entrez databases, explore searchable fields within a specific database, or identify cross-database links for building EDirect queries.
EnglishUse when converting GenBank Flat files to structured info output for downstream parsing or analysis.
EnglishUse when converting legacy Novoalign text output into SAM, especially for unique alignments and optional paired-end interpretation.
EnglishUse when filtering RNAsubopt -s output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.
EnglishUse when identifying and masking low-complexity regions in protein sequences with the SEG algorithm before BLAST or other downstream analyses.
EnglishUse when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.
EnglishUse when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.
EnglishUse when converting NCBI C toolkit BLAST command lines to NCBI C++ toolkit equivalents.
UncertainUse when aligning RNA-seq reads to a reference genome or generating splice-aware genome indices for transcript alignment.
Latin
AGENT SKILLS ATLASIncludes Bowtie2 Inspect, Combine Uid Lists, Ecommon Sh, and other workflows.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Bowtie2 Inspect
Use when you need to extract reference sequences, names, or summary information from a Bowtie2 index file.
Combine Uid Lists
Use when unioning multiple Entrez or NCBI UID files into one deduplicated numeric-sorted list.
Ct2db
Use when converting RNA connectivity-table (.ct) files into extended FASTA with dot-bracket structures, optionally removing pseudoknots or modified bases.
Ecommon Sh
Use when auditing or reusing the shared EDirect shell functions that other Entrez Direct wrapper scripts source internally.
Einfo
Use when you need to discover available NCBI Entrez databases, explore searchable fields within a specific database, or identify cross-database links for building EDirect queries.
Gbf2info
Use when converting GenBank Flat files to structured info output for downstream parsing or analysis.
Novo2sam Pl
Use when converting legacy Novoalign text output into SAM, especially for unique alignments and optional paired-end interpretation.
Popt
Use when filtering RNAsubopt -s output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.
Segmasker
Use when identifying and masking low-complexity regions in protein sequences with the SEG algorithm before BLAST or other downstream analyses.
Sublong
Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.
Vcf Concat
Use when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.
Legacy Blast Pl
Use when converting NCBI C toolkit BLAST command lines to NCBI C++ toolkit equivalents.
Star Ssse3
Use when aligning RNA-seq reads to a reference genome or generating splice-aware genome indices for transcript alignment.
Quick start
- Choose your skills. Select individual skills above, or choose the entire pack.
- Copy the install prompt. Use Copy install prompt above the list.
- Send it to your agent. Paste into your coding agent’s chat. Your agent reviews the source and guides the setup.
Try it with your agent
After installation, start with a request like:
Use the Bowtie2 Inspect skill to help with my task.
Ask me for the context you need before getting started.Requirements & license
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- Your agent checks each skill’s instructions, dependencies, and permissions during setup.
- Reported license for the skills shown: MIT. The author’s terms apply.