Nextflow Modules
Showing module(s) with keyword "umi"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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/chelae/trim | Process | trimming quality control fastq adapter umi | Adapter and quality trimming of short-read FASTQ data using chelae. |
| nf-core/fastq_create_umi_consensus_fgbio | Workflow | fgbio umi samblaster samtools bwa | This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads convert them to unmapped BAM file, map them to the reference genome, and finally use the mapped information to group UMIs and generate consensus reads in each group |
| nf-core/fgbio/callduplexconsensusreads | Process | umi duplex fgbio | Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule. |
| nf-core/fgbio/copyumifromreadname | Process | fgbio copy umi readname | Copies the UMI at the end of a bam files read name to the RX tag. |
| nf-core/fgbio/filterconsensusreads | Process | fgbio filter consensus umi duplexumi | Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. |
| nf-core/fgbio/zipperbams | Process | fgbio umi unmapped ubam zipperbams | FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM |
| nf-core/fgumi/duplex | Process | umi duplex consensus bam | Calls duplex consensus sequences from reads generated from the same double-stranded source molecule. This is a high-performance replacement for fgbio CallDuplexConsensusReads. |
| nf-core/fgumi/extract | Process | umi extract fastq bam | Extract unique molecular indices (UMIs) from FASTQ files and write an unaligned BAM file. |
| nf-core/fgumi/filter | Process | umi filter consensus bam | Filters consensus reads generated by simplex or duplex consensus calling. This is a high-performance replacement for fgbio FilterConsensusReads. |
| nf-core/fgumi/group | Process | umi groupreads bam | Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5' mapping positions of the reads from the template. Reads that have the same end positions are then sub-grouped by UMI sequence. This is a high-performance replacement for fgbio GroupReadsByUmi. |
| nf-core/fgumi/simplex | Process | umi consensus simplex bam | Calls simplex consensus sequences from reads with the same unique molecular tag. This is a high-performance replacement for fgbio CallMolecularConsensusReads. |
| nf-core/humid | Process | umi fastq deduplication hamming-distance clustering | HUMID is a tool to quickly and easily remove duplicate reads from FASTQ files, with or without UMIs. |
| nf-core/mako | Process | sort bam sam template-coordinate umi | Sort SAM/BAM files by coordinate, queryname or template-coordinate using a fast external merge-sort |
| nf-core/ultraplex | Process | demultiplex fastq umi | Ultraplex is an all-in-one software package for processing and demultiplexing fastq files. |
| nf-core/umitools/group | Process | umitools umi deduplication dedup clustering | Group reads based on their UMI and mapping coordinates |
| nf-core/universc | Process | demultiplex align single-cell scRNA-Seq count umi | Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data |