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

TagOtherFile #

Marks reads based on whether ’they’ are present in another file.

Supports comparing by read sequence, read name, and tags.

[[step]]
 action = "TagOtherFile"
 source = 'read1' # <segment>, name:<segment> or tag<tag_name>
 out_label = "present_in_other_file"
 filename = "names.fastq" # Can read fastq (also compressed), or SAM/BAM, or fasta files
 false_positive_rate = 0.01 # false positive rate (0..1)
 seed = 42 # seed for randomness
 include_mapped = true # in case of BAM/SAM, whether to include aligned reads
 include_unmapped = true # in case of BAM/SAM, whether to include unaligned reads
 # other_read_name_end_character " " # in name: mode, Cut the other files read names at this character

This step annotates reads by comparing them to another file.

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

FilterDuplicates #

[[step]]
 action = "TagDuplicates"
 false_positive_rate = 0.00001 #
 # the false positive rate of the filter.
 # 0..1
 seed = 59 # required!
 source = "All" # Any input segment, 'All', 'tag:<tag-name>' or 'name:<segment>'
 # split_character = "/" # required (and accepted only iff using name:<segment>
 out_label = "dups"
 # initial_filter_capacity = 10_000_000 # optional. Auto detected by default

[[step]]
 action = "FilterByTag"
 in_label = "dups"
 keep_or_remove = "Remove" # Keep|Remove

Tag duplicates (2nd onwards) from the stream using a Cuckoo filter.

Boolean Tag Generation on fastqrab documentation

TagOtherFile #

FilterDuplicates #