Tools for working with genomic and high throughput sequencing data.

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Group: FASTQ

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 (--output-type BamOnly), gzipped FASTQ (--output-type FastqOnly), or both (--output-type 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 -. A metrics file will also be output providing analogous information to the metric described SampleBarcodeMetric.

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 _R1.fastq.gz and _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 read should be given:

Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:

  1. T identifies a template read
  2. B identifies a sample barcode read
  3. M identifies a unique molecular index read
  4. S identifies a set of bases that should be skipped or ignored

The last <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 the - 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 BC tag.

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.

Sample Sheet

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:

  * Sample_ID:      The sample identifier unique to the sample in the sample sheet.
  * Sample_Name:    The sample name.
  * Library_ID:     The library Identifier.  The combination sample name and library identifier should be unique
                    across the samples in the sample sheet.
  * Description:    The description of the sample, which will be placed in the description field in the output BAM's
                    read group.  This column may be omitted.
  * Sample_Barcode: The sample barcode bases unique to each sample. The name of the column containing the sample barcode 
                    can be changed using the `--column-for-sample-barcode` option.  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.

## Metadata CSV

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 (`Sample_ID`, `Sample_Name`, `Library_ID`, and

## Example Command Line

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 \ –sample-sheet SampleSheet.csv –metrics metrics.txt –output output_folder ```

Illumina FASTQ File Naming

The output FASTQs will be written according to Illumina naming standards when the --illumina-standards option is specified. This requires that the input fastq files contain Illumina format read names with comments containing <ReadNum>:<FilterFlag>:<0>:<SampleNumber> (no angle brackets). The output create output files with Illumina names:

  1. The file extension will be _R1_001.fastq.gz for read one, and _R2_001.fastq.gz for read two (if paired end).
  2. The per-sample output prefix will be <SampleName>_S<SampleOrdinal>_L<LaneNumber> (without angle brackets).


Name Flag Type Description Required? Max 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 demux_barcode_metrics.txt will be written to the output directory. Optional 1  
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 <flowcell-barcode>-<sample-barcode>.<lane>) Optional 1  
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  
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  
output-fastqs   Boolean ** Deprecated: use –output-type instead **. Output gzipped FASTQs (.fastq.gz) instead of BAM files Optional 1  
illumina-standards   Boolean Output FASTQs according to Illumina naming standards, for example, for upload to the BaseSpace Sequence Hub Optional 1 false
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