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Tools & Automation
CLI tools, utilities, converters, workflow automation, and productivity helpers
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Showing 2,617–2,640 of 46,837 skills
- Bio Workflows Riboseq PipelineEnd-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.Votes: 0GitHub stars: 2
- Bio Workflows Genome Assembly PipelineEnd-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.Votes: 0GitHub stars: 2
- Bio Workflows Clip PipelineEnd-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods.Votes: 0GitHub stars: 2
- Bio Vcf StatisticsGenerate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.Votes: 0GitHub stars: 2
- Bio Vcf ManipulationMerge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.Votes: 0GitHub stars: 2
- Bio Variant NormalizationNormalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.Votes: 0GitHub stars: 2
- Bio Variant CallingCall SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.Votes: 0GitHub stars: 2
- Bio Sequence SlicingSlice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.Votes: 0GitHub stars: 2
- Bio Ribo Seq Ribosome StallingDetect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon-specific translation dynamics.Votes: 0GitHub stars: 2
- Bio Ribo Seq Ribosome PeriodicityValidate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determining read offsets for downstream analysis.Votes: 0GitHub stars: 2
- Bio Ribo Seq Riboseq PreprocessingPreprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.Votes: 0GitHub stars: 2
- Bio Reference OperationsGenerate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.Votes: 0GitHub stars: 2
- Bio Read Qc Umi ProcessingExtract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.Votes: 0GitHub stars: 2
- Bio Primer Design Primer BasicsDesign 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.Votes: 0GitHub stars: 2
- Bio Pileup GenerationGenerate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.Votes: 0GitHub stars: 2
- Bio Pdb Structure IoParse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.Votes: 0GitHub stars: 2
- Bio Paired End FastqHandle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.Votes: 0GitHub stars: 2
- Bio Multi Omics Similarity NetworkSimilarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity networks.Votes: 0GitHub stars: 2
- Bio Microbiome Qiime2 WorkflowQIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.Votes: 0GitHub stars: 2
- Bio Methylation Bismark AlignmentBisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.Votes: 0GitHub stars: 2
- Bio Longread MedakaPolish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.Votes: 0GitHub stars: 2
- Bio Genome Assembly Hifi AssemblyHigh-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.Votes: 0GitHub stars: 2
- Bio Format ConversionConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.Votes: 0GitHub stars: 2
- Bio Filter SequencesFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.Votes: 0GitHub stars: 2