hisat2/hisat2_align

Alignment

RNA-seq

HISAT2

Description

Align reads to a reference genome using HISAT2.
Outputs SAM files containing the alignment.

Inputs

Name	Type & Properties	Description
--index_dir	file required	Directory containing the HISAT2 index files (.1.ht2 through .8.ht2).
--index_prefix	string required	Prefix name for the 8 index files inside the index directory.
--input	file required multiple	For single-end, the reads file(s). For paired-end, the R1 (forward) reads file(s). Provide multiple files to align them together as one sample.
--input_r2	file multiple	R2 (reverse) reads file(s) for paired-end alignment. If omitted, single-end mode is used. Provide multiple files to align them together as one sample.

Name

Type & Properties

--index_dir

file

required

--index_prefix

string

required

--input

file

required

multiple

--input_r2

file

multiple

Outputs

Name	Type & Properties	Description
--output_sam	file required output	Output SAM file containing alignments.
--novel_splicesite_outfile	file output	Report a list of splice sites discovered during alignment to this file.
--summary_file	file output	Print alignment summary statistics to this file.

Name

Type & Properties

--output_sam

file

required

output

--novel_splicesite_outfile

file

output

--summary_file

file

output

Input Format

Name	Type & Properties	Description
--fasta -f	boolean_true	Input reads are in FASTA format. Default expects FASTQ.
--qseq	boolean_true	Input reads are in Illumina QSEQ format.
--phred64	boolean_true	Input quality scores are Phred+64 encoded. Default is Phred+33.
--int_quals	boolean_true	Input quality scores are encoded as space-separated integers.
--skip -s	integer	Skip the first N reads or read pairs in the input.
--qupto -u	integer	Align only the first N reads or read pairs. Default processes all reads.
--trim5	integer	Trim N bases from the 5' (left) end of each read before alignment.
--trim3	integer	Trim N bases from the 3' (right) end of each read before alignment.

Name

Type & Properties

--fasta

-f

boolean_true

--qseq

boolean_true

--phred64

boolean_true

--int_quals

boolean_true

--skip

-s

integer

--qupto

-u

integer

--trim5

integer

--trim3

integer

Paired-end Options

Name	Type & Properties	Description
--minins -I	integer	Minimum fragment length for valid paired-end alignment. Default is 0.
--maxins -X	integer	Maximum fragment length for valid paired-end alignment. Default is 500.
--fr	boolean_true	Paired-end mates are oriented forward/reverse (default).
--rf	boolean_true	Paired-end mates are oriented reverse/forward.
--ff	boolean_true	Paired-end mates are oriented forward/forward.
--no_mixed	boolean_true	Suppress unpaired alignments for paired reads that fail to align concordantly.
--no_discordant	boolean_true	Suppress discordant alignments for paired reads.
--dovetail	boolean_true	Treat dovetailing mates as concordant.
--no_contain	boolean_true	Not concordant if one mate is contained within the other.
--no_overlap	boolean_true	Not concordant if mates overlap at all.

Name

Type & Properties

--minins

-I

integer

--maxins

-X

integer

--fr

boolean_true

--rf

boolean_true

--ff

boolean_true

--no_mixed

boolean_true

--no_discordant

boolean_true

--dovetail

boolean_true

--no_contain

boolean_true

--no_overlap

boolean_true

Alignment Options

Name	Type & Properties	Description
--end_to_end	boolean_true	End-to-end alignment mode; entire read must align (default).
--local	boolean_true	Local alignment mode; soft clipping of ends is allowed.
--very_fast	boolean_true	Preset for very fast end-to-end alignment (low sensitivity).
--fast	boolean_true	Preset for fast end-to-end alignment.
--sensitive	boolean_true	Preset for sensitive end-to-end alignment (default).
--very_sensitive	boolean_true	Preset for very sensitive end-to-end alignment (high sensitivity, slower).
--very_fast_local	boolean_true	Preset for very fast local alignment (low sensitivity).
--fast_local	boolean_true	Preset for fast local alignment.
--sensitive_local	boolean_true	Preset for sensitive local alignment.
--very_sensitive_local	boolean_true	Preset for very sensitive local alignment (high sensitivity, slower).
--n_ceil	string	Function governing max number of ambiguous characters (N) allowed in a read. Default: L,0,0.15.
--dpad	integer	Pad dynamic programming problems by N extra reference columns on either side. Default is 15.
--gbar	integer	Disallow gaps within N positions of the read start or end. Default is 4.
--ignore_quals	boolean_true	Treat all base quality values as the highest possible when calculating mismatch penalties.
--nofw	boolean_true	Do not attempt to align the forward strand of reads.
--norc	boolean_true	Do not attempt to align the reverse-complement strand of reads.
--no_1mm_upfront	boolean_true	Disable the 1-mismatch-per-seed policy applied before dynamic programming.

Name

Type & Properties

--end_to_end

boolean_true

--local

boolean_true

--very_fast

boolean_true

--fast

boolean_true

--sensitive

boolean_true

--very_sensitive

boolean_true

--very_fast_local

boolean_true

--fast_local

boolean_true

--sensitive_local

boolean_true

--very_sensitive_local

boolean_true

--n_ceil

string

--dpad

integer

--gbar

integer

--ignore_quals

boolean_true

--nofw

boolean_true

--norc

boolean_true

--no_1mm_upfront

boolean_true

Spliced Alignment Options

Name	Type & Properties	Description
--no_spliced_alignment	boolean_true	Disable spliced alignment; treat the genome as a flat reference.
--rna_strandness	string	Specify strand-specific information: F (forward), R (reverse), FR, or RF.
--tmo	boolean_true	Report only alignments within the known transcriptome (transcriptome-mapping-only).
--dta	boolean_true	Report alignments tailored for downstream transcript assembly (e.g. StringTie).
--dta_cufflinks	boolean_true	Report alignments tailored for Cufflinks downstream assembly.
--avoid_pseudogene	boolean_true	Avoid alignment to pseudogene regions.
--no_templatelen_adjustment	boolean_true	Disable template length adjustment for RNA-seq pairs.
--known_splicesite_infile	file	Provide a file of known splice sites to guide alignment.
--novel_splicesite_infile	file	Provide a file of novel splice sites (e.g. from a prior run) to use during alignment.
--no_temp_splicesite	boolean_true	Do not use temporary splice sites discovered in earlier reads to inform later alignments.
--secondary_alignments	boolean_true	Report secondary alignments.
--pen_cansplice	integer	Penalty for a canonical splice site (GT/AG). Default is 0.
--pen_noncansplice	integer	Penalty for a non-canonical splice site. Default is 12.
--pen_canintronlen	string	Penalty function for canonical intron length. Default: G,-8,1.
--pen_noncanintronlen	string	Penalty function for non-canonical intron length. Default: G,-8,1.
--min_intronlen	integer	Minimum intron length. Default is 20.
--max_intronlen	integer	Maximum intron length. Default is 500000.

Name

Type & Properties

--no_spliced_alignment

boolean_true

--rna_strandness

string

--tmo

boolean_true

--dta

boolean_true

--dta_cufflinks

boolean_true

--avoid_pseudogene

boolean_true

--no_templatelen_adjustment

boolean_true

--known_splicesite_infile

file

--novel_splicesite_infile

file

--no_temp_splicesite

boolean_true

--secondary_alignments

boolean_true

--pen_cansplice

integer

--pen_noncansplice

integer

--pen_canintronlen

string

--pen_noncanintronlen

string

--min_intronlen

integer

--max_intronlen

integer

Scoring Options

Name	Type & Properties	Description
--ma	integer	Match bonus in local alignment mode. Default is 2.
--mp	integer multiple	Max and min mismatch penalties as MX,MN. Default: 6,2.
--sp	integer multiple	Max and min soft-clipping penalties for local mode as MX,MN. Default: 1,0.
--np	integer	Penalty for aligning against an ambiguous (N) character. Default is 1.
--rdg	integer multiple	Read gap open and extend penalties as open,extend. Default: 5,3.
--rfg	integer multiple	Reference gap open and extend penalties as open,extend. Default: 5,3.
--score_min	string	Function for minimum acceptable alignment score. Default: L,0,-0.2 (end-to-end); G,20,8 (local).

Name

Type & Properties

--ma

integer

--mp

integer

multiple

--sp

integer

multiple

--np

integer

--rdg

integer

multiple

--rfg

integer

multiple

--score_min

string

Reporting Options

Name	Type & Properties	Description
--k -k	integer	Report up to N alignments per read. Default reports the best alignment only.
--all -a	boolean_true	Report all valid alignments per read.
--max_seeds	integer	Maximum number of seeds to try extending per read. Default is 5.

Name

Type & Properties

--k

-k

integer

--all

-a

boolean_true

--max_seeds

integer

SAM Options

Name	Type & Properties	Description
--no_unal	boolean_true	Suppress SAM records for reads that fail to align.
--no_hd	boolean_true	Suppress SAM header lines (lines beginning with @).
--no_sq	boolean_true	Suppress @SQ SAM header lines.
--rg_id	string	Set the read group ID; causes an @RG header line with this ID to appear in SAM output.
--rg	string multiple	Add a field (TAG:VALUE) to the @RG SAM header line. Can be specified multiple times.
--omit_sec_seq	boolean_true	Put * in the SEQ and QUAL fields for secondary alignments to reduce output size.
--sam_no_qname_trunc	boolean_true	Suppress read-name truncation (by default names longer than 255 characters are truncated).
--xeq	boolean_true	Use = and X CIGAR operations instead of M to distinguish matches from mismatches.
--soft_clipped_unmapped_tlen	boolean_true	Set TLEN field to 0 for soft-clipped reads that are otherwise unmapped.
--add_chrname	boolean_true	Add "chr" prefix to reference sequence names in SAM output.
--remove_chrname	boolean_true	Remove "chr" prefix from reference sequence names in SAM output.

Name

Type & Properties

--no_unal

boolean_true

--no_hd

boolean_true

--no_sq

boolean_true

--rg_id

string

--rg

string

multiple

--omit_sec_seq

boolean_true

--sam_no_qname_trunc

boolean_true

--xeq

boolean_true

--soft_clipped_unmapped_tlen

boolean_true

--add_chrname

boolean_true

--remove_chrname

boolean_true

Other Options

Name	Type & Properties	Description
--new_summary	boolean_true	Print alignment summary to stderr in a machine-friendly tab-separated format.
--quiet -q	boolean_true	Print nothing to stderr except serious errors.
--reorder	boolean_true	Force SAM output to appear in the same order as the input reads.
--mm	boolean_true	Use memory-mapped I/O to load the index (useful when aligning many samples concurrently).
--seed	integer	Seed for the pseudo-random number generator. Default is 0.

Name

Type & Properties

--new_summary

boolean_true

--quiet

-q

boolean_true

--reorder

boolean_true

--mm

boolean_true

--seed

integer

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_sam: "$id.$key.output_sam.sam"  
novel_splicesite_outfile: "$id.$key.novel_splicesite_outfile.txt"  
summary_file: "$id.$key.summary_file.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/hisat2/hisat2_align/main.nf \  
  -params-file params.yaml

hisat2/hisat2_align

Inputs

Outputs

Input Format

Paired-end Options

Alignment Options

Spliced Alignment Options

Scoring Options

Reporting Options

SAM Options

Other Options

Run this component

Relationships

Used by

Uses