Nextflow Modules
Showing module(s) with keyword "index"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/arcane/index | Process | single-cell rnaseq index kmer hash transcriptomics | Build a k-mer hash index from a filtered reference for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/bam_dedup_stats_samtools_umicollapse | Workflow | umi dedup index bam sam cram | umicollapse, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_dedup_stats_samtools_umitools | Workflow | umi dedup index bam sam cram | UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_split_by_region | Workflow | split bam sam cram index | Split the reads in the input bam by specified genomic region. |
| nf-core/bam_variant_calling_sort_freebayes_bcftools | Workflow | variant sort index bam cram vcf | Call variants using freebayes, then sort and index |
| nf-core/bbmap/index | Process | map index fasta | Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode. |
| nf-core/bcftools/index | Process | vcf index bcftools csi tbi | Index VCF tools |
| nf-core/biscuit/index | Process | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index reference fasta | Indexes a reference genome for use with Biscuit |
| nf-core/biscuit/qc | Process | 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 | Process | 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 | Process | build index fasta genome reference | Builds bowtie index for reference genome |
| nf-core/bowtie/build | Process | index fasta genome reference | Create bowtie index for reference genome |
| nf-core/bwafastalign/index | Process | index fasta genome reference | Create BWA-FASTALIGN index for reference genome |
| nf-core/bwa/index | Process | index fasta genome reference | Create BWA index for reference genome |
| nf-core/bwamem2/index | Process | index fasta genome reference | Create BWA-mem2 index for reference genome |
| nf-core/bwamem3/index | Process | index fasta genome reference | Create bwa-mem3 index for reference genome |
| nf-core/bwameme/index | Process | index fasta genome |