Parametersandtheirdefaults:
ow=f (overwrite) Overwrites files that already exist.
app=f (append) Append to files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f (interleaved) Determines whether INPUT file is considered interleaved.
fastawrap=70
Length of lines in fasta output.
fastareadlen=0
Set to a non-zero number to break fasta files into reads of at most this length.
fastaminlen=1
Ignore fasta reads shorter than this.
qin=auto
ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
qout=auto
ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
qfake=30
Quality value used for fasta to fastq reformatting.
qfin=<.qual file>
Read qualities from this qual file, for the reads coming from 'in=<fasta file>'
qfin2=<.qual file>
Read qualities from this qual file, for the reads coming from 'in2=<fasta file>'
qfout=<.qual file>
Write qualities from this qual file, for the reads going to 'out=<fasta file>'
qfout2=<.qual file>
Write qualities from this qual file, for the reads coming from 'out2=<fasta file>'
outsingle=<file>
(outs) If a read is longer than minlength and its mate is shorter, the longer one goes here.
deleteinput=f
Delete input upon successful completion.
ref=<file>
Optional reference fasta for sam processing.
ProcessingParameters
verifypaired=f
(vpair) When true, checks reads to see if the names look paired. Prints an error message if not.
verifyinterleaved=f
(vint) sets 'vpair' to true and 'interleaved' to true.
allowidenticalnames=f
(ain) When verifying pair names, allows identical names, instead of requiring /1 and /2 or 1: and
2:
tossbrokenreads=f
(tbr) Discard reads that have different numbers of bases and qualities. By default this will be
detected and cause a crash.
ignorebadquality=f
(ibq) Fix out-of-range quality values instead of crashing with a warning.
addslash=f
Append ' /1' and ' /2' to read names, if not already present. Please include the flag 'int=t' if
the reads are interleaved.
spaceslash=t
Put a space before the slash in addslash mode.
addcolon=f
Append ' 1:' and ' 2:' to read names, if not already present. Please include the flag 'int=t' if
the reads are interleaved.
underscore=f
Change whitespace in read names to underscores.
rcomp=f
(rc) Reverse-complement reads.
rcompmate=f
(rcm) Reverse-complement read 2 only.
comp=f (complement) Reverse-complement reads.
changequality=t
(cq) N bases always get a quality of 0 and ACGT bases get a min quality of 2.
quantize=f
Quantize qualities to a subset of values like NextSeq. Can also be used with comma-delimited
list, like quantize=0,8,13,22,27,32,37
tuc=f (touppercase) Change lowercase letters in reads to uppercase.
uniquenames=f
Make duplicate names unique by appending _<number>.
remap= A set of pairs: remap=CTGN will transform C>T and G>N.
Use remap1 and remap2 to specify read 1 or 2.
iupacToN=f
(itn) Convert non-ACGTN symbols to N.
monitor=f
Kill this process if it crashes. monitor=600,0.01 would kill after 600 seconds under 1% usage.
crashjunk=t
Crash when encountering reads with invalid bases.
tossjunk=f
Discard reads with invalid characters as bases.
fixjunk=f
Convert invalid bases to N (or X for amino acids).
dotdashxton=f
Specifically convert . - and X to N (or X for amino acids). fixheaders=f Convert nonstandard
header characters to standard ASCII.
recalibrate=f
(recal) Recalibrate quality scores. Must first generate matrices with CalcTrueQuality.
maxcalledquality=41
Quality scores capped at this upper bound.
mincalledquality=2
Quality scores of ACGT bases will be capped at lower bound.
trimreaddescription=f
(trd) Trim the names of reads after the first whitespace.
trimrname=f
For sam/bam files, trim rname/rnext fields after the first space.
fixheaders=f
Replace characters in headers such as space, *, and | to make them valid file names.
warnifnosequence=t
For fasta, issue a warning if a sequenceless header is encountered.
warnfirsttimeonly=t
Issue a warning for only the first sequenceless header.
utot=f Convert U to T (for RNA -> DNA translation).
padleft=0
Pad the left end of sequences with this many symbols.
padright=0
Pad the right end of sequences with this many symbols.
pad=0 Set padleft and padright to the same value.
padsymbol=N
Symbol to use for padding.
Histogramoutputparameters
bhist=<file>
Base composition histogram by position.
qhist=<file>
Quality histogram by position.
qchist=<file>
Count of bases with each quality value.
aqhist=<file>
Histogram of average read quality.
bqhist=<file>
Quality histogram designed for box plots.
lhist=<file>
Read length histogram.
gchist=<file>
Read GC content histogram.
gcbins=100
Number gchist bins. Set to 'auto' to use read length.
gcplot=f
Add a graphical representation to the gchist.
maxhistlen=6000
Set an upper bound for histogram lengths; higher uses more memory.
The default is 6000 for some histograms and 80000 for others.
Histogramsforsamfilesonly(requiressamformat1.4orhigher):
ehist=<file>
Errors-per-read histogram.
qahist=<file>
Quality accuracy histogram of error rates versus quality score.
indelhist=<file>
Indel length histogram.
mhist=<file>
Histogram of match, sub, del, and ins rates by read location.
ihist=<file>
Insert size histograms. Requires paired reads in a sam file.
idhist=<file>
Histogram of read count versus percent identity.
idbins=100
Number idhist bins. Set to 'auto' to use read length.
Samplingparameters
reads=-1
Set to a positive number to only process this many INPUT reads (or pairs), then quit.
skipreads=-1
Skip (discard) this many INPUT reads before processing the rest.
samplerate=1
Randomly output only this fraction of reads; 1 means sampling is disabled.
sampleseed=-1
Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
samplereadstarget=0
(srt) Exact number of OUTPUT reads (or pairs) desired.
samplebasestarget=0
(sbt) Exact number of OUTPUT bases desired.
Important: srt/sbt flags should not be used with stdin, samplerate, qtrim, minlength, or
minavgquality.
upsample=f
Allow srt/sbt to upsample (duplicate reads) when the target is greater than input.
prioritizelength=f
If true, calculate a length threshold to reach the target, and retain all reads of at least that
length (must set srt or sbt).
Trimmingandfilteringparameters
qtrim=f
Trim read ends to remove bases with quality below trimq.
Values: t (trim both ends), f (neither end), r (right end only), l (left end only), w (sliding
window).
trimq=6
Regions with average quality BELOW this will be trimmed. Can be a floating-point number like 7.3.
minlength=0
(ml) Reads shorter than this after trimming will be discarded. Pairs will be discarded only if
both are shorter.
mlf=0 (mlf) Reads shorter than this fraction of original length after trimming will be discarded.
maxlength=0
If nonzero, reads longer than this after trimming will be discarded.
breaklength=0
If nonzero, reads longer than this will be broken into multiple reads of this length. Does not
work for paired reads.
requirebothbad=t
(rbb) Only discard pairs if both reads are shorter than minlen.
invertfilters=f
(invert) Output failing reads instead of passing reads.
minavgquality=0
(maq) Reads with average quality (after trimming) below this will be discarded.
maqb=0 If positive, calculate maq from this many initial bases.
chastityfilter=f
(cf) Reads with names containing ' 1:Y:' or ' 2:Y:' will be discarded.
barcodefilter=f
Remove reads with unexpected barcodes if barcodes is set, or barcodes containing 'N' otherwise.
A barcode must be the last part of the read header.
barcodes=
Comma-delimited list of barcodes or files of barcodes.
maxns=-1
If 0 or greater, reads with more Ns than this (after trimming) will be discarded.
minconsecutivebases=0
(mcb) Discard reads without at least this many consecutive called bases.
forcetrimleft=0
(ftl) If nonzero, trim left bases of the read to this position (exclusive, 0-based).
forcetrimright=-1
(ftr) If nonnegative, trim right bases of the read after this position (exclusive, 0-based).
forcetrimright2=0
(ftr2) If positive, trim this many bases on the right end.
forcetrimmod=5
(ftm) If positive, trim length to be equal to zero modulo this number.
mingc=0
Discard reads with GC content below this.
maxgc=1
Discard reads with GC content above this.
gcpairs=t
Use average GC of paired reads.
Also affects gchist.
Tag-filteringparameters:
tag= Look for this tag in the header to filter by the next value. To filter reads with a header like
'foo,depth=5.5,bar' where you only want depths of at least 3, the necessary flags would be
'tag=depth= minvalue=3 delimiter=,'
delimiter=
Character after the end of the value, such as delimiter=X. Control and whitespace symbols may be
spelled out, like delimiter=tab or delimiter=pipe. The tag may contain the delimiter. If the
value is the last term in the header, the delimiter doesn't matter but is still required.
minvalue=
If set, only accept a numeric value of at least this.
maxvalue=
If set, only accept a numeric value of at most this.
value= If set, only accept a string value of exactly this.
Illumina-specificparameters:
top=true
Include reads from the top of the flowcell.
bottom=true
Include reads from the bottom of the flowcell.
Samandbamprocessingoptions:
mappedonly=f
Toss unmapped reads.
unmappedonly=f
Toss mapped reads.
pairedonly=f
Toss reads that are not mapped as proper pairs.
unpairedonly=f
Toss reads that are mapped as proper pairs.
primaryonly=f
Toss secondary alignments. Set this to true for sam to fastq conversion.
minmapq=-1
If non-negative, toss reads with mapq under this.
maxmapq=-1
If non-negative, toss reads with mapq over this.
requiredbits=0
(rbits) Toss sam lines with any of these flag bits unset. Similar to samtools -f.
filterbits=0
(fbits) Toss sam lines with any of these flag bits set. Similar to samtools -F.
stoptag=f
Set to true to write a tag indicating read stop location, prefixed by YS:i:
sam= Set to 'sam=1.3' to convert '=' and 'X' cigar symbols (from sam 1.4+ format) to 'M'.
Set to 'sam=1.4' to convert 'M' to '=' and 'X' (sam=1.4 requires MD tags to be present, or ref to
be specified).
Samandbamalignmentfilteringoptions:
These require = and X symbols in cigar strings, or MD tags, or a reference fasta. -1 means disabled; to
filter reads with any of a symbol type, set to 0.
subfilter=-1
Discard reads with more than this many substitutions.
minsubs=-1
Discard reads with fewer than this many substitutions.
insfilter=-1
Discard reads with more than this many insertions.
delfilter=-1
Discard reads with more than this many deletions.
indelfilter=-1
Discard reads with more than this many indels.
editfilter=-1
Discard reads with more than this many edits.
inslenfilter=-1
Discard reads with an insertion longer than this.
dellenfilter=-1
Discard reads with a deletion longer than this.
minidfilter=-1.0
Discard reads with identity below this (0-1).
maxidfilter=1.0
Discard reads with identity above this (0-1).
clipfilter=-1
Discard reads with more than this many soft-clipped bases.
Kmercountingandcardinalityestimation:
k=0 If positive, count the total number of kmers.
cardinality=f
(loglog) Count unique kmers using the LogLog algorithm.
loglogbuckets=1999
Use this many buckets for cardinality estimation.
Shortcuts
The # symbol will be substituted for 1 and 2. The % symbol in out will be substituted for input name
minus extensions. For example:
reformat.sh in=read#.fq out=%.fa
...is equivalent to:
reformat.sh in1=read1.fq in2=read2.fq out1=read1.fa out2=read2.fa
JavaParameters-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. The max is typically 85%
of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java
8u92+.
-da Disable assertions.
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