Expand description
Consensus calling and filtering for UMI-based molecular consensus reads
This crate provides comprehensive functionality for generating consensus sequences from reads grouped by Unique Molecular Identifiers (UMIs). It includes:
- Base-level consensus calling: Building consensus bases from multiple reads
- Duplex consensus: Calling duplex consensus from paired single-strand consensuses
- Simple UMI consensus: Fast consensus for non-overlapping reads
- Vanilla consensus: Standard consensus without special features
- Overlapping consensus: Handling overlapping read pairs
- Consensus filtering: Quality-based filtering and masking of consensus reads
- Consensus tags: SAM tags for tracking consensus metrics
Re-exports§
pub use base_builder::ConsensusBaseBuilder;pub use caller::ConsensusCaller;pub use caller::calculate_error_rate;pub use caller::log_consensus_statistics;pub use filter::ConsensusType;pub use filter::FilterConfig;pub use filter::FilterResult;pub use filter::FilterThresholds;pub use filter::compute_read_stats;pub use filter::count_no_calls;pub use filter::filter_duplex_read;pub use filter::filter_read;pub use filter::is_duplex_consensus;pub use filter::mask_bases;pub use filter::mask_duplex_bases;pub use filter::mean_base_quality;pub use filter::template_passes;pub use overlapping::AgreementStrategy;pub use overlapping::CorrectionStats;pub use overlapping::DisagreementStrategy;pub use overlapping::OverlappingBasesConsensusCaller;pub use overlapping::apply_overlapping_consensus;pub use sequence::ConsensusSequence;pub use vanilla_caller::VanillaConsensusRead;pub use vanilla_caller::VanillaUmiConsensusCaller;pub use vanilla_caller::VanillaUmiConsensusOptions;pub use duplex_caller::DuplexConsensusCaller;pub use duplex_caller::DuplexConsensusRead;pub use codec_caller::CodecConsensusCaller;pub use codec_caller::CodecConsensusOptions;pub use codec_caller::CodecConsensusStats;
Modules§
- base_
builder - Consensus Base Calling
- caller
- Consensus Calling Infrastructure
- codec_
caller - CODEC Consensus Calling
- duplex_
caller - Duplex Consensus Calling
- filter
- Consensus read filtering logic.
- overlapping
- Overlapping bases consensus caller for paired-end reads.
- phred
- Phred score utilities and probability calculations.
- sequence
- Consensus sequence data structure.
- simple_
umi - Simple UMI consensus calling for metrics collection.
- tags
- Consensus-related SAM tags for reads generated by consensus calling tools.
- vanilla_
caller - Vanilla UMI consensus calling implementation.