Nextflow Modules
Showing module(s) with keyword "stats"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_stats_mirna_mirtop | Workflow | miRNA isomirs bam stats | mirtop is a command line tool to annotate miRNAs and isomiRs and compute general statistics using the mirGFF3 format. |
| nf-core/bamtools/stats | Process | bamtools stats bam | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bcftools/plotvcfstats | Process | visualization stats VCF | Plots the output of bcftools stats |
| nf-core/bcftools/stats | Process | variant calling stats VCF | Generates stats from VCF files |
| nf-core/custom/collectstats | Process | stats collect summary qc | Collects per-sample read-processing statistics (trimming, decontamination, alignment, feature counting, and optionally taxonomy/function summaries) from a set of heterogeneous log/table files into a single overall-stats table per run. |
| nf-core/fastq_shortreads_preprocess_qc | Workflow | fastq illumina short reads qc stats preprocessing barcoding adapters merge complexity deduplication host decontamination | Quality check and preprocessing subworkflow of Illumina short reads that can do: quality check of input reads and generate statistics, preprocess and validate reads, barcode removal, remove adapters and merge reads, filter by sequence complexity, deduplicate reads, remove host contamination, concatenate reads and generate statistics for post-processing reads. WARNING: requires at least the process configurations from the nextflow.config to be added to the modules.config in the pipeline in order to work as intended. |
| nf-core/gt/stat | Process | genome gff3 annotation statistics stats | GenomeTools gt-stat utility to show statistics about features contained in GFF3 files |
| nf-core/ltrretriever/lai | Process | genomics annotation repeat long terminal retrotransposon retrotransposon stats qc | Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments |
| nf-core/pairtools/stats | Process | stats pairs pairsam | Calculate pairs statistics |
| nf-core/sambamba/flagstat | Process | stats flagstat sambamba | Outputs some statistics drawn from read flags. |
| nf-core/samtools/flagstat | Process | stats mapping counts bam sam cram | Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type |
| nf-core/samtools/idxstats | Process | stats mapping counts chromosome bam sam cram | Reports alignment summary statistics for a BAM/CRAM/SAM file |
| nf-core/seqfu/stats | Process | seqfu stats n50 | Statistics for FASTA or FASTQ files |
| nf-core/seqkit/stats | Process | seqkit fasta stats | simple statistics of FASTA/Q files |
| nf-core/vcf_extract_relate_somalier | Workflow | somalier stats vcf ped relatedness | Perform somalier extraction and relate stats on input VCFs |
| nf-core/whatshap/stats | Process | vcf whatshap stats phasing phase | Compute statistics from phased variant file using Whatshap |