Nextflow Modules
Showing module(s) with keyword "bqsr"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_applybqsr | Workflow | bam cram bqsr recalibration gatk4 | Apply Base Quality Score Recalibration (BQSR) to a BAM or CRAM file using GATK4 ApplyBQSR. Supports scatter-gather across genomic intervals: when more than one interval file is supplied per sample, the interval-level outputs are merged back together with samtools merge. When no intervals are supplied (num_intervals: 0), ApplyBQSR is run once on the whole input and no merge step is performed. |
| nf-core/gatk4/analyzecovariates | Process | bqsr gatk4 genomics | Evaluate and compare base quality score recalibration (BQSR) tables |
| nf-core/gatk4/applybqsr | Process | bam base quality score recalibration bqsr cram gatk4 | Apply base quality score recalibration (BQSR) to a bam file |
| nf-core/gatk4/baserecalibrator | Process | base quality score recalibration table bqsr gatk4 sort | Generate recalibration table for Base Quality Score Recalibration (BQSR) |
| nf-core/gatk4/gatherbqsrreports | Process | base quality score recalibration bqsr gatherbqsrreports gatk4 | Gathers scattered BQSR recalibration reports into a single file |
| nf-core/gatk4spark/applybqsr | Process | bam base quality score recalibration bqsr cram gatk4spark | Apply base quality score recalibration (BQSR) to a bam file |
| nf-core/gatk4spark/baserecalibrator | Process | base quality score recalibration table bqsr gatk4spark sort | Generate recalibration table for Base Quality Score Recalibration (BQSR) |
| nf-core/parabricks/applybqsr | Process | bqsr bam GPU-accelerated base quality score recalibration | NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR). |
| nf-core/parabricks/fq2bam | Process | align sort bqsr duplicates | NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked. |
| nf-core/parabricks/fq2bammeth | Process | align sort bqsr duplicates bwameth | NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence |
| nf-core/parabricks/minimap2 | Process | align sort bqsr duplicates long read | NVIDIA Clara Parabricks GPU-accelerated minimap2 for aligning long read sequences against a large reference database using an accelerated KSW2 to convert FASTQ to BAM/CRAM. |
| nf-core/sentieon/qualcal | Process | base quality score recalibration bqsr sentieon | Generate recalibration table and optionally perform base quality recalibration |