Nextflow Modules
Showing module(s) with keyword "index"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bbmap/index | map index fasta | Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode. |
| nf-core/bcftools/index | vcf index bcftools csi tbi | Index VCF tools |
| nf-core/biscuit/index | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index reference fasta | Indexes a reference genome for use with Biscuit |
| nf-core/biscuit/qc | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index BAM quality control | Perform basic quality control on a BAM file generated with Biscuit |
| nf-core/bismark/genomepreparation | bismark 3-letter genome index methylation 5mC methylseq bisulphite bisulfite fasta | Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments. |
| nf-core/bowtie2/build | build index fasta genome reference | Builds bowtie index for reference genome |
| nf-core/bowtie/build | index fasta genome reference | Create bowtie index for reference genome |
| nf-core/bwa/index | index fasta genome reference | Create BWA index for reference genome |
| nf-core/bwamem2/index | index fasta genome reference | Create BWA-mem2 index for reference genome |
| nf-core/bwameme/index | index fasta genome reference | Create BWA-MEME index for reference genome |
| nf-core/bwameth/index | bwameth 3-letter genome index methylseq bisulphite bisulfite fasta | Performs indexing of c2t converted reference genome |
| nf-core/cellrangerarc/mkgtf | reference mkref index | Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command. |
| nf-core/cellrangerarc/mkref | reference mkref index | Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command. |
| nf-core/cellrangeratac/mkref | reference mkref index | Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command. |
| nf-core/cellranger/mkgtf | reference mkref index | Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command. |
| nf-core/cellranger/mkref | reference mkref index | Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command. |
| nf-core/cellranger/mkvdjref | reference mkvdjref index immunoprofiling single-cell cellranger | Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command. |
| nf-core/chromap/index | index fasta genome reference | Indexes a fasta reference genome ready for chromatin profiling. |
| nf-core/cobs/classicconstruct | COBS index k-mer index bloom filter | Builds a classic bloom filter COBS index |
| nf-core/cobs/compactconstruct |