Browse Secure Claude Skills
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- Write Sequences--> --- name: bio-write-sequences description: Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Write SeqRecord objects to sequence files using Biopython's Bio.SeqIO module.Votes: 0GitHub stars: 6
- Sequence Statistics--> --- name: bio-sequence-statistics description: Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Calculate comprehensive statistics for sequence datasets using Biopython.Votes: 0GitHub stars: 6
- Read Sequences--> --- name: bio-read-sequences description: Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Read biological sequence data from files us...Votes: 0GitHub stars: 6
- Paired End Fastq--> --- name: bio-paired-end-fastq description: Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Handle paired-end sequencing data (R1/R2 files) using Biopython.Votes: 0GitHub stars: 6
- Format Conversion--> --- name: bio-format-conversion description: Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Convert sequence files between formats using Biopython's Bio.SeqIO module.Votes: 0GitHub stars: 6
- Filter Sequences--> --- name: bio-filter-sequences description: Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Filter and select sequences based on various criteria using Biopython.Votes: 0GitHub stars: 6
- Fastq Quality--> --- name: bio-fastq-quality description: Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Analyze and manipulate FASTQ quality scores using Biopython.Votes: 0GitHub stars: 6
- Compressed Files--> --- name: bio-compressed-files description: Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files. tool_type: python primary_tool: Bio.bgzf measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Handle gzip, bzip2, and BGZF compressed sequence files with Biopython.Votes: 0GitHub stars: 6
- Batch Processing--> --- name: bio-batch-processing description: Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Process multiple sequence files efficiently using Biopython.Votes: 0GitHub stars: 6
- Restriction Sites--> --- name: bio-restriction-sites description: Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or circular DNA. Use when finding restriction enzyme cut sites in sequences. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file...Votes: 0GitHub stars: 6
- Restriction Mapping--> --- name: bio-restriction-mapping description: Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps. Use when creating or analyzing restriction maps. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Fragment Analysis--> --- name: bio-restriction-fragment-analysis description: Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Enzyme Selection--> --- name: bio-restriction-enzyme-selection description: Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning. Use when selecting restriction enzymes for cloning or analysis. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file -...Votes: 0GitHub stars: 6
- Qpcr Primers--> --- name: bio-primer-design-qpcr-primers description: Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assays. Use when designing qPCR primers and probes. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Design primers and internal probes...Votes: 0GitHub stars: 6
- Primer Validation--> --- name: bio-primer-design-primer-validation description: Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability. Use when validating primer specificity and properties. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command -...Votes: 0GitHub stars: 6
- Primer Basics--> --- name: bio-primer-design-primer-basics description: Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Returns ranked primer pairs with quality metrics. Use when designing standard PCR primers. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Design PCR primers ...Votes: 0GitHub stars: 6
- Pairwise Alignment--> --- name: bio-alignment-pairwise description: Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences. tool_type: python primary_tool: Bio.Align measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Align two sequences ...Votes: 0GitHub stars: 6
- Msa Statistics--> --- name: bio-alignment-msa-statistics description: Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns. tool_type: python primary_tool: Bio.Align measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Calculate sequence id...Votes: 0GitHub stars: 6
- Msa Parsing--> --- name: bio-alignment-msa-parsing description: Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments. tool_type: python primary_tool: Bio.AlignIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_co...Votes: 0GitHub stars: 6
- Sam Bam Basics--> --- name: bio-sam-bam-basics description: View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure. tool_type: cli primary_tool: samtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- View and convert alignment files using samtools and pysam.Votes: 0GitHub stars: 6