Nextflow Modules
Showing module(s) with keyword "indexing"
| Module | Keywords | Description |
|---|---|---|
| nf-core/custom/getchromsizes | fasta chromosome indexing | Generates a FASTA file of chromosome sizes and a fasta index file |
| nf-core/folddisco/index | protein structure structural motif motif search geometric hashing indexing pdb mmcif | Build a geometric-hashing index of discontinuous structural motifs from a directory of protein structure files |
| nf-core/hmmer/eslsfetchindex | hmmer easel indexing sequence retrieval ssi index fasta | Builds an SSI (sequence/subsequence index) file for a sequence file, using the esl-sfetch utility, an Easel miniapp bundled with the HMMER package (esl-sfetch --index). The resulting index lets esl-sfetch retrieve sequences from the file in constant time. This module is the indexing half of a pair: hmmer/eslsfetchindex builds the SSI index, hmmer/eslsfetch consumes it (or an equivalent one) to fetch sequences or subsequences. |
| nf-core/mmseqs/cluster | protein sequence databases clustering searching indexing mmseqs2 | Cluster sequences using MMSeqs2 cluster. |
| nf-core/mmseqs/createdb | protein sequence databases clustering searching indexing mmseqs2 | Create an MMseqs database from an existing FASTA/Q file |
| nf-core/mmseqs/createindex | protein sequence databases clustering searching indexing | Creates sequence index for mmseqs database |
| nf-core/mmseqs/createtsv | protein sequence databases clustering searching indexing mmseqs2 tsv | Create a tsv file from a query and a target database as well as the result database |
| nf-core/mmseqs/databases | database indexing clustering searching | Download an mmseqs-formatted database |
| nf-core/mmseqs/linclust | protein sequence databases clustering searching indexing mmseqs2 | Cluster sequences in linear time using MMSeqs2 linclust. |
| nf-core/mmseqs/makepaddedseqdb | protein sequence databases clustering searching indexing mmseqs2 | Create an MMseqs padded database from an existing MMseqs database |
| nf-core/mmseqs/search | protein sequence databases clustering searching indexing mmseqs2 | Search and calculate a score for similar sequences in a query and a target database. |
| nf-core/mmseqs/tsv2exprofiledb | protein sequence databases clustering searching indexing | Conversion of expandable profile to databases to the MMseqs2 databases format |
| nf-core/simpleaf/index | indexing transcriptome gene expression SimpleAF | Indexing of transcriptome for gene expression quantification using SimpleAF |
| nf-core/svdss/index | structural variants sv calling indexing reference genome fm-index | Index a reference genome FASTA file using SVDSS (via ropebwt3), producing either an FMD or FMR index for use with SVDSS smooth and search subcommands |
| nf-core/sylph/sketch | sketch metagenomics sylph indexing | Sketching/indexing sequencing reads |
| nf-core/sylph/sketchsamples | sketch metagenomics sylph samples indexing | Sketching/indexing sequencing reads |