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vimalinx

@vimalinx source repo

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1. ▌
   Star · vimalinx bundle

   Use when aligning spliced RNA-seq reads to a reference genome, generating genome indices, or performing splice-aware alignment for transcriptome analysis.
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   Bgzip · vimalinx bundle

   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.
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   Ct2db · vimalinx bundle

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

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

   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.
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   Elink · vimalinx bundle

   Use when you need to navigate relationships between records in NCBI Entrez databases, find related articles, track citations, or link records across different databases such as PubMed to Protein.
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   Epost · vimalinx bundle

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

   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.
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   Mafft · vimalinx bundle

   Use when performing multiple sequence alignment on nucleotide or protein sequences, such as preparing alignments for phylogenetic analysis or comparative genomics.
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    Md5fa · vimalinx bundle

    Use when hashing FASTA records and comparing ordered versus order-insensitive sequence digests instead of taking a single whole-file MD5.
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    Rnaup · vimalinx bundle

    Use when calculating thermodynamics of RNA-RNA interactions, including accessibility and binding energy predictions for RNA duplex formation.
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    Seqtk · vimalinx bundle

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

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

    Use when simulating paired-end short reads from a reference FASTA for testing, benchmarking, or pipeline validation
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    Xinfo · vimalinx bundle

    Use when inspecting fields, indexed terms, or term counts from a local EDirect postings index rather than the remote `einfo` endpoint.
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    Xlink · vimalinx bundle

    Use when following local EDirect link relations such as PubMed `CITED`, `CITES`, or `PMCID` from an incoming UID stream or `ENTREZ_DIRECT` message.
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    Biomni · vimalinx

    Use when working from the local Biomni repository to run agent-style biomedical tasks or inspect Biomni's biomedical tool modules and examples.
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