Tools for working with genomic and high throughput sequencing data.

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Group: FASTQ

Generates an unmapped BAM (or SAM or CRAM) file from fastq files. Takes in one or more fastq files (optionally gzipped), each representing a different sequencing read (e.g. R1, R2, I1 or I2) and can use a set of read structures to allocate bases in those reads to template reads, sample indices, unique molecular indices, or to designate bases to be skipped over.

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. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:

--input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B

Alternative if you know your reads are of fixed length you could specify:

--input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B

For more information on read structures see the Read Structure Wiki Page

UMIs may be extracted from the read sequences, the read names, or both. If --extract-umis-from-read-names is specified, any UMIs present in the read names are extracted; read names are expected to be :-separated with any UMIs present in the 8th field. If this option is specified, the --umi-qual-tag option may not be used as qualities are not available for UMIs in the read name. If UMI segments are present in the read structures those will also be extracted. If UMIs are present in both, the final UMIs are constructed by first taking the UMIs from the read names, then adding a hyphen, then the UMIs extracted from the reads.

The same number of input files and read structures must be provided, with one exception: if supplying exactly 1 or 2 fastq files, both of which are solely template reads, no read structures need be provided.

The output file can be sorted by queryname using the --sort-order option; the default is to produce a BAM with reads in the same order as they appear in the fastq file.


Name Flag Type Description Required? Max # of Values Default Value(s)
input i PathToFastq Fastq files corresponding to each sequencing read (e.g. R1, I1, etc.). Required Unlimited  
output o PathToBam The output SAM or BAM file to be written. Required 1  
read-structures r ReadStructure Read structures, one for each of the FASTQs. Optional Unlimited  
sort s Boolean If true, queryname sort the BAM file, otherwise preserve input order. Optional 1 false
umi-tag u String Tag in which to store molecular barcodes/UMIs. Optional 1 RX
umi-qual-tag q String Tag in which to store molecular barcode/UMI qualities. Optional 1  
store-sample-barcode-qualities Q Boolean Store the sample barcode qualities in the QT Tag. Optional 1 false
extract-umis-from-read-names n Boolean Extract UMI(s) from read names and prepend to UMIs from reads. Optional 1 false
read-group-id   String Read group ID to use in the file header. Optional 1 A
sample   String The name of the sequenced sample. Required 1  
library   String The name/ID of the sequenced library. Required 1  
barcode b String Library or Sample barcode sequence. Optional 1  
platform   String Sequencing Platform. Optional 1 illumina
platform-unit   String Platform unit (e.g. ‘..') Optional 1  
platform-model   String Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX) 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  
description   String Description of the read group. Optional 1  
comment   String Comment(s) to include in the output file’s header. Optional Unlimited  
run-date   Iso8601Date Date the run was produced, to insert into the read group header Optional 1