REQUIRED OPTIONS:¶

-b [--bcl-dir]

Illumina's BaseCalls directory which contains the sequence information of the reads.

-i [--index]

Path to the HiLive index.

-r [--reads]

Length and types of the read segments.

Required options might be specified either on the command line or in the config file.

GENERAL OPTIONS:¶

-h [ --help ]

Print this help message and exit.

-l [ --license ]

Print license information and exit.

-c [ --config ] arg

Path to a config file. Config file is in .ini format. Duplicate keys are not permitted. Instead, use comma-separated lists. Parameters obtained from the command line are prioritized over settings made in the config file.

Example for a config.ini:

bcl-dir=./BaseCalls lanes=1 out-cycle=50,100

--runinfo arg

Path to Illumina's runInfo.xml file. If specified, read lengths, lane count and tile count are automatically set in accordance with the sequencing run. Parameters obtained from the command line or config file are prioritized over settings obtained from the runInfo.xml.

--continue arg

Continue an interrupted HiLive run from a specified cycle. We strongly recommend to load the config file that was automatically created for the original run to continue with identical settings. This config file (hilive_config.ini) can be found in the temporary directory specified with --temp-dir.

SEQUENCING OPTIONS:¶

-b [ --bcl-dir ] arg

Illumina's BaseCalls directory which contains the sequence information of the reads.

-l [ --lanes ] arg

Specify the lanes to be considered for read alignment. [Default: 1-8]

-t [ --tiles ] arg

Specify the tiles to be considered for read alignment. [Default: [1-2][1-3][01-16] (96 tiles)]

-T [ --max-tile ] arg

Specify the highest tile number. The tile numbers will be computed by this number, considering the correct surface count, swath count and tile count for Illumina sequencing. This parameter serves as a shortcut for --tiles.

Example:

--max-tile 2216

will activate all tiles in

[1-2][1-2][01-16].

-r [ --reads ] arg

Length and types of the read segments. Each segment is either a read ('R') or a barcode ('B'). Please give the segments in the correct order as they are produced by the sequencing machine. [REQUIRED]

Example:

--reads 101R,8B,8B,101R

specifies paired-end sequencing with

2x101bp reads and 2x8bp barcodes.

-B [ --barcodes ] arg

Barcode(s) of the sample(s) to be considered for read alignment. Barcodes must match the barcode length(s) as specified with --reads. Delimit different segments of the same barcodes by '-' and different barcodes by ','. [Default: All barcodes]

Example:

-b ACCG-ATTG,ATGT-TGAC

for two different barcodes of length 2x4bp.

--run-id arg

ID of the sequencing run. Should be obtained from runInfo.xml.

--flowcell-id arg

ID of the flowcell. Should be obtained from runInfo.xml.

--instrument-id arg

ID of the sequencing machine. Should be obtained from runInfo.xml.

REPORT OPTIONS:¶

-o [ --out-dir ] arg

Path to the directory that is used for the output files. The directory will be created if it does not exist. [Default: ./out]

-f [ --out-format ] arg

Format of the output files. Currently, SAM and BAM format are supported. [Default: BAM]

-O [ --out-cycles ] arg

Cycles for that alignment output is written. The respective temporary files are kept. [Default: write only after the last cycle]

-M [ --out-mode ] arg

The output mode. [Default: ANYBEST] [ALL|A]: Report all found alignments. [BESTN#|N#]: Report the # best found alignments. [ALLBEST|H]: Report all found alignments with the best score. [ANYBEST|B]: Report one best alignment. [UNIQUE|U]: Report only unique alignments.

--report-unmapped

Activate reporting unmapped reads. [Default: false]

--extended-cigar

Activate extended CIGAR format for the alignment output files ('=' for matches and 'X' for mismatches instead of using 'M' for both). [Default: false]

--force-resort

Always sort temporary alignment files before writing output. Existing sorted align files are overwritten. This is only necessary if the temp directory is used more than once for new alignments. In general, this is not recommended for most applications. [Default: false (only sort if no sorted files exist)]

--max-softclip-ratio arg

Maximal relative length of the front softclip (only relevant during output) [Default: 0.2]

Further explanation:

HiLive uses an approach that requires one exact match of a k-mer at the beginning of an alignment. This can lead to unaligned regions at the beginning of the read which we report as 'softclips'. With this parameter, you can control the maximal length of this region.

ALIGNMENT OPTIONS:¶

-i [ --index ] arg

Path to the HiLive index. Please use the executable 'hilive-build' to create a new HiLive index that is delivered with this program. The index consists of several files with the same prefix. Please include the file prefix when specifying the index location.

-m [ --align-mode ] arg

Alignment mode to balance speed and accuracy [very-fast|fast|balanced|accurate| very-accurate]. This selected mode automatically sets other parameters. Individually configured parameters are prioritized over settings made by selecting an alignment mode. [Default: balanced]

--anchor-length arg

Length of the alignment anchor (or initial seed) [Default: set by the selected alignment mode]

--error-interval arg

The interval to tolerate more errors during alignment (low=accurate; great=fast). [Default: 'anchor-length'/2]

--seeding-interval arg

The interval to create new seeds (low=accurate; great=fast). [Default: 'anchor-length'/2]

--max-softclip-length arg

The maximum length of a front softclip when creating new seeds. In contrast to --max-softclip-ratio, this parameter may have effects on runtime and mapping accuracy. [Default: 'readlength/2]

--barcode-errors arg

The number of errors that are tolerated for the barcode segments. A single value can be provided to be applied for all barcode segments. Alternatively, the value can be set for each segment individually. [Default: 1]

Example:

--barcode-errors 2 [2 errors for all barcode segments]

--barcode-errors 2,1 [2 errors for the first, 1 error for the second segment]

--align-undetermined-barcodes

Align all barcodes. Reads with a barcode that don't match one of the barcodes specified with '--barcodes' will be reported as undetermined. [Default: false]

--min-basecall-quality arg

Minimum basecall quality for a nucleotide to be considered as a match [Default: 1 (everything but N-calls)]

--keep-invalid-sequences

Keep sequences of invalid reads, i.e. with unconsidered barcode or filtered by the sequencer. This option must be activated to report unmapped reads. [Default: false]

SCORING OPTIONS:¶

-s [ --min-as ] arg

Minimum alignment score. [Default: Set automatically based on the alignment mode and match/mismatch scores]

--match-score arg

Score for a match. [Default: 0]

--mismatch-penalty arg

Penalty for a mismatch. [Default: 6]

--insertion-opening-penalty arg

Penalty for insertion opening. [Default: 5]

--insertion-extension-penalty arg Penalty for insertion extension. [Default: 3]

--deletion-opening-penalty arg

Penalty for deletion opening. [Default: 5]

--deletion-extension-penalty arg

Penalty for deletion extension. [Default: 3]

--max-gap-length arg

Maximal permitted consecutive gap length. Increasing this parameter may lead to highly increased runtime! [Default: 3]

--softclip-opening-penalty arg

Penalty for softclip opening (only relevant during output). [Default: 'mismatch-penalty']

--softclip-extension-penalty arg

Penalty for softclip extension (only relevant during output). [Default: 'mismatch-penalty'/'anchor-length']

TECHNICAL OPTIONS:¶

--temp-dir arg

Temporary directory to store the alignment files and hilive_config.ini. [Default: ./temp]

-k [ --keep-files ] arg

Keep intermediate alignment files for these cycles. The last cycle is always kept. [Default: Keep files of output cycles]

Further Explanations:

HiLive comes with a separated executable 'hilive-out'. This executable can be used to produce alignment files in SAM or BAM format from existing temporary files. Thus, output can only be created for cycles for that keeping the temporary alignment files is activated. Temporary alignment files are also needed if an interrupted run is continued with the '--continue' parameter.

-K [ --keep-all-files ]

Keep all intermediate alignment files. This option may lead to huge disk space requirements. [Default: false]

--block-size arg

Block size for the alignment input/output stream in Bytes. Append 'K' or 'M' to specify in Kilobytes or Megabytes, respectively. [Default: 64M]

Example:

--block-size 1024 [1024 bytes] --block-size 64K [64 Kilobytes] --block-size 64M [64 Megabytes]

--compression arg

Compression of temporary alignment files. [Default: LZ4] 0: no compression. 1: Deflate (smaller). 2: LZ4 (faster).

-n [ --num-threads ] arg

Number of threads to spawn (including output threads). [Default: 1]

-N [ --num-out-threads ] arg

Maximum number of threads to use for output. More threads may be used for output automatically if threads are idle. [Default: 'num-threads'/2]