Region Tag Generation on mbf-fastq-processor documentation

Mon, 01 Jan 0001 00:00:00 +0000

ExtractAnchor #

Extract regions relative to a previously tagged anchor position.

# First create an anchor tag. Iupac, regex, ExtractRegion, your choice.
[[step]]
 action = "ExtractIUPAC"
 search = "CAYA"
 out_label = "anchor_tag"
 segment = "read1"
 anchor = "Anywhere"
 max_mismatches = 0

# Then extract relative to that anchor
[[step]]
 action = "ExtractAnchor"
 out_label = "mytag"
 in_label = "anchor_tag" # tag that provides the anchor position
 regions = [[-2, 4], [4, 1]] # [start, length] pairs relative to anchor
 region_separator = "_" # (optional) separator between regions

This transformation uses the leftmost position of a previously established tag as the anchor point and extracts specified regions relative to that position.

Mon, 01 Jan 0001 00:00:00 +0000

ExtractRegex #

Extract a regexp result. Stores an empty string if not found.

[[step]]
 action = "ExtractRegex"
 out_label = "mytag"
 search = "^CT(..)CT"
 replacement = "$1" # standard regex replacement syntax
 source = "read1" # An input segment (to read from sequence), or name:<segment> to read from a tag

This transformation searches for a regular expression pattern in the specified read and extracts the matching portion as a tag.

The value actually ’extracted’ is after replacement has been performed.

Mon, 01 Jan 0001 00:00:00 +0000

ExtractRegion #

Extract a fixed position region.

[[step]]
 action = "ExtractRegion"
 start = 5
 length = 8
 segment = "read1" # Any of your input segments
 out_label = "umi"

This transformation extracts a fixed-length region from the specified read at a given position and stores it as a tag.

Use ExtractRegions if your region is actually multiple regions (possibly from different segments).

If the read is shorter than requested, the region will be shorter (and might be of varying length).

Mon, 01 Jan 0001 00:00:00 +0000

ExtractRegions #

Extract from multiple fixed position regions.

[[step]]
 action = "ExtractRegions"
 regions = [
 {segment = "read1", start = 0, length = 8},
 {segment = "read1", start = 12, length = 4},
 ]
 out_label = "barcode"

This transformation extracts multiple fixed-length regions from reads and concatenates them into a single tag.

ExtractRegions with only one region are exactly equivalent to ExtractRegion.

If the read is shorter than requested, the region will be shorter (and might be of varying length).

Mon, 01 Jan 0001 00:00:00 +0000

ExtractRegionsOfLowQuality #

Extract regions (min size 1 bp) where bases have quality scores below threshold.

[[step]]
 action = "ExtractRegionsOfLowQuality"
 segment = "read1" # Any of your input segments
 min_quality = 60 # Quality threshold (Phred+33)
 out_label = "low_quality_regions"

This transformation scans through quality scores of the specified segment and identifies contiguous regions where quality scores are below the specified threshold. Each low-quality region becomes a tagged region with location information (start position and length).

Parameters #

segment: Which read to analyze for low-quality regions
min_quality: Quality score threshold using Phred+33 encoding. See Phred quality score for ASCII character mapping
out_label: Tag name to store the extracted regions

Example #

With min_quality = 60 (ASCII ‘<’), any bases with quality scores below ‘<’ will be identified as low-quality regions. This is useful for masking or filtering poor-quality sequences.

Extract IUPAC

Mon, 01 Jan 0001 00:00:00 +0000

ExtractIUPAC #

[[step]]
 action = "ExtractIUPAC"
 out_label = "mytag"
 anchor = 'Left' # Left | Right | Anywhere
 search = "CTN" # what we are searching
 segment = 'read1' # Any of your input segments

Search and extract a sequence from the read, defined by a IUPAC string.

If anchor = ‘Anywhere’, ExtractIUPAC will find the left most occurance.

Extract IUPAC suffix

Mon, 01 Jan 0001 00:00:00 +0000

ExtractIUPACSuffix #

[[step]]
 action = "ExtractIUPACSuffix"
 out_label = "mytag"
 query = "AGTCA" # the adapter to trim. Straigth bases only, no IUPAC.
 segment = "read1" # Any of your input segments (default: read1)
 min_length = 3 # uint, the minimum length of match between the end of the read and
 # the start of the adapter
 max_mismatches = 1 # How many mismatches to accept

Find a potentially truncated IUPAC string sequence at the end of a read.

Simple comparison with a max mismatch hamming distance, requiring only the first min length bases of the query to match at the end of the read.

Extract IUPAC with Indels

Mon, 01 Jan 0001 00:00:00 +0000

ExtractIUPACWithIndel #

[[step]]
 action = "ExtractIUPACWithIndel"
 out_label = "adapter"
 search = "AGTC" # IUPAC pattern to align against
 max_mismatches = 1 # allowed substitutions (IUPAC-aware)
 max_indel_bases = 1 # total insertions + deletions allowed
 max_total_edits = 2 # optional overall edit ceiling
 anchor = 'Anywhere' # Left | Right | Anywhere
 segment = 'read1' # defaults to read1

Locate an IUPAC pattern even when the read contains small insertions or deletions relative to the pattern. The extractor performs a semiglobal alignment (pattern vs. read segment) using IUPAC-aware scoring and returns the aligned span as a location tag.

Mon, 01 Jan 0001 00:00:00 +0000

ExtractLongestPolyX #

Find the longest homopolymer stretch anywhere in the read (unlike ExtractPolyTail, which only considers suffixes).

[[step]]
 action = "ExtractLongestPolyX"
 out_label = "my_tag"
 segment = "read1"
 min_length = 5
 base = '.' # search for any homopolymer (A/C/G/T/N)
 max_mismatch_rate = 0.15
 max_consecutive_mismatches = 2

base accepts a concrete nucleotide (A, C, G, T, N) or . to search all of ACGT and report the longest hit.
max_mismatch_rate and max_consecutive_mismatches mirror ExtractPolyTail; they control how permissive the run detection is.
When no run satisfies min_length, the tag is reported as missing.
only one run is reported, even if multiple runs of the same length exist; in this case, the first run found is reported.

Mon, 01 Jan 0001 00:00:00 +0000

TrimQualityEnd #

[[step]]
 action = "ExtractLowQualityEnd"
 out_label = "low_quality_ends"
 min_qual = 20 # u8, minimum quality to keep (in whatever your score is encoded in)
 # either a char like 'A' or a number 0..128 (typical phred score is 33..75)
 segment = "read1" # Any of your input segments

Define a region of low quality bases at the end of reads.

Corresponding options in other software #

Trimmomatic: TRAILING (if paired with TrimAtTag)

Mon, 01 Jan 0001 00:00:00 +0000

TrimQualityStart #

[[step]]
 action = "ExtractLowQualityStart"
 min_qual = 20 # u8, minimum quality to keep (in whatever your score is encoded in)
 # either a char like 'A' or a number 0..128 (typical phred score is 33..75)
 segment = "read1" # Any of your input segments
 out_label = "bad_starts"

Define a region with low quality bases (below threshold) at steart of read.

Corresponding options in other software #

Trimmomatic: LEADING (if combined with TrimAtTag)

Mon, 01 Jan 0001 00:00:00 +0000

ExtractPolyTail #

[[step]]
 action = "ExtractPolyTail"
 out_label = "tag_label"
 segment = "read1" # Any of your input segments (default: read1)
 min_length = 5 # positive integer, the minimum number of repeats of the base
 base = "A" # one of AGTCN., the 'base' to trim (or . for any repeated base)
 max_mismatch_rate = 0.1 # float 0.0..=1.0, how many mismatches are allowed in the repeat
 max_consecutive_mismatches = 3 # how many consecutive mismatches are allowed

Identify either a specific letter (AGTC or N) repetition, or any base repetition (base = ‘.’) at the end of the read.