Performs sample demultiplexing on FASTQs.
The sample barcode for each sample in the sample sheet will be compared against the sample barcode bases extracted from the FASTQs, to assign each read to a sample. Reads that do not match any sample within the given error tolerance will be placed in the ‘unmatched’ file.
The type of output is specified with the
--output-type option, and can be BAM (
gzipped FASTQ (
--output-type Fastq), or both (
For BAM output, the output directory will contain one BAM file per sample in the sample sheet or metadata CSV file,
plus a BAM for reads that could not be assigned to a sample given the criteria. The output file names will be the
concatenation of sample id, sample name, and sample barcode bases (expected not observed), delimited by
metrics file will also be output providing analogous information to the metric described
For gzipped FASTQ output, one or more gzipped FASTQs per sample in the sample sheet or metadata CSV file will be
written to the output directory. For paired end data, the output will have the suffix
_R2.fastq.gz for read one and read two respectively. The sample barcode and molecular barcodes (concatenated)
will be appended to the read name and delimited by a colon. If the
--illumina-standards option is given, then
the output read names and file names will follow the
Illumina standards described here.
The output base qualities will be standardized to Sanger/SAM format.
FASTQs and associated read structures for each sub-read should be given:
If multiple FASTQs are present for each sub-read, then the FASTQs for each sub-read should be concatenated together
prior to running this tool (ex.
cat s_R1_L001.fq.gz s_R1_L002.fq.gz > s_R1.fq.gz).
(Read structures)[https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures] are made up of
pairs much like the
CIGAR string in BAM files. Four kinds of operators are recognized:
Tidentifies a template read
Bidentifies a sample barcode read
Midentifies a unique molecular index read
Sidentifies a set of bases that should be skipped or ignored
<number><operator> pair may be specified using a
+ sign instead of number to denote “all remaining
bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. Both reads must
have template bases. Any molecular identifiers will be concatenated using
- delimiter and placed in the given SAM record tag (
RX by default). Similarly, the sample barcode bases
from the given read will be placed in the
Metadata about the samples should be given in either an Illumina Experiment Manager sample sheet or a metadata CSV file. Formats are described in detail below.
The read structures will be used to extract the observed sample barcode, template bases, and molecular identifiers from each read. The observed sample barcode will be matched to the sample barcodes extracted from the bases in the sample metadata and associated read structures.
The read group’s sample id, sample name, and library id all correspond to the similarly named values in the
sample sheet. Library id will be the sample id if not found, and the platform unit will be the sample name
concatenated with the sample barcode bases delimited by a
The sample section of the sample sheet should contain information related to each sample with the following columns:
--column-for-sample-barcodeoption. If the sample barcode is present across multiple reads (ex. dual-index, or inline in both reads of a pair), then the expected barcode bases from each read should be concatenated in the same order as the order of the reads’ FASTQs and read structures given to this tool.
In lieu of a sample sheet, a simple CSV file may be provided with the necessary metadata. This file should
contain the same columns as described above for the sample sheet (
As an example, if the sequencing run was 2x100bp (paired end) with two 8bp index reads both reading a sample barcode, as well as an in-line 8bp sample barcode in read one, the command line would be
--inputs r1.fq i1.fq i2.fq r2.fq --read-structures 8B92T 8B 8B 100T \ --metadata SampleSheet.csv --metrics metrics.txt --output output_folder
The following options affect the output format:
--omit-fastq-read-numbersis specified, then trailing /1 and /2 for R1 and R2 respectively, will not be appended to e FASTQ read name. By default they will be appended.
--include-sample-barcodes-in-fastqis specified, then sample barcode will replace the last field in the first comment in the FASTQ header, e.g. replace ‘NNNNNN’ in the header
--illumina-file-namesis specified, the output files will be named according to the Illumina FASTQ file naming conventions:
a. The file extension will be
_R1_001.fastq.gz for read one, and
_R2_001.fastq.gz for read two (if paired end).
b. The per-sample output prefix will be
<SampleName>_S<SampleOrdinal>_L<LaneNumber> (without angle brackets).
Options (1) and (2) require the input FASTQ read names to contain the following elements:
@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index>
--illumina-standards option may not be specified with the three options above. Use this option if you
intend to upload to Illumina BaseSpace. This option implies:
--omit-fastq-read-numbers=true --include-sample-barcodes-in-fastq=false --illumina-file-names=true
To output with recent Illumina conventions (circa 2021) that match
--omit-fastq-read-numbers=true --include-sample-barcodes-in-fastq=true --illumina-file-names=true
By default all input reads are output. If your input FASTQs contain reads that do not pass filter (as defined by the Y/N filter flag in the FASTQ comment) these can be filtered out during demultiplexing using the
To output only reads that are not control reads, as encoded in the
<control number> field in the header comment, use the
|Name||Flag||Type||Description||Required?||Max # of Values||Default Value(s)|
|inputs||i||PathToFastq||One or more input fastq files each corresponding to a sub-read (ex. index-read, read-one, read-two, fragment).||Required||Unlimited|
|output||o||DirPath||The output directory in which to place sample BAMs.||Required||1|
|metadata||x||FilePath||A file containing the metadata about the samples.||Required||1|
|read-structures||r||ReadStructure||The read structure for each of the FASTQs.||Required||Unlimited|
|metrics||m||FilePath||The file to which per-barcode metrics are written. If none given, a file named
|column-for-sample-barcode||c||String||The column name in the sample sheet or metadata CSV for the sample barcode.||Optional||1||Sample_Barcode|
|unmatched||u||String||Output BAM file name for the unmatched records.||Optional||1||unmatched.bam|
|quality-format||q||QualityEncoding||A value describing how the quality values are encoded in the FASTQ. Either Solexa for pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33. If this value is not specified, the quality format will be detected automatically.||Optional||1|
|threads||t||Int||The number of threads to use while de-multiplexing. The performance does not increase linearly with the # of threads and seems not to improve beyond 2-4 threads.||Optional||1||1|
|max-mismatches||Int||Maximum mismatches for a barcode to be considered a match.||Optional||1||1|
|min-mismatch-delta||Int||Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.||Optional||1||2|
|max-no-calls||Int||Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.||Optional||1||2|
|sort-order||SortOrder||The sort order for the output sam/bam file (typically unsorted or queryname).||Optional||1||queryname|
|umi-tag||String||The SAM tag for any molecular barcode. If multiple molecular barcodes are specified, they will be concatenated and stored here.||Optional||1||RX|
|platform-unit||String||The platform unit (typically
|sequencing-center||String||The sequencing center from which the data originated||Optional||1|
|predicted-insert-size||Integer||Predicted median insert size, to insert into the read group header||Optional||1|
|platform-model||String||Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)||Optional||1|
|platform||String||Platform to insert into the read group header of BAMs (e.g Illumina)||Optional||1||Illumina|
|comments||String||Comment(s) to include in the merged output file’s header.||Optional||Unlimited|
|run-date||Iso8601Date||Date the run was produced, to insert into the read group header||Optional||1|
|output-type||OutputType||The type of outputs to produce.||Optional||1|
|include-all-bases-in-fastqs||Boolean||Output all bases (i.e. all sample barcode, molecular barcode, skipped, and template bases) for every read with template bases (ex. read one and read two) as defined by the corresponding read structure(s).||Optional||1||false|
|illumina-standards||Boolean||Output FASTQs according to Illumina BaseSpace Sequence Hub naming standards. This is differfent than Illumina naming standards.||Optional||1||false|
|omit-fastq-read-numbers||Boolean||Do not include trailing /1 or /2 for R1 and R2 in the FASTQ read name.||Optional||1||false|
|include-sample-barcodes-in-fastq||Boolean||Insert the sample barcode into the FASTQ header.||Optional||1||false|
|illumina-file-names||Boolean||Name the output files according to the Illumina file name standards.||Optional||1||false|
|omit-failing-reads||Boolean||Keep only passing filter reads if true, otherwise keep all reads. Passing filter reads are determined from the comment in the FASTQ header.||Optional||1||false|
|omit-control-reads||Boolean||Do not keep reads identified as control if true, otherwise keep all reads. Control reads are determined from the comment in the FASTQ header.||Optional||1||false|
|mask-bases-below-quality||Int||Mask bases with a quality score below the specified threshold as Ns||Optional||1||0|