lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh
Written by Brian Bushnell
Last modified July 16, 2018
Description: Uses kmer counts to assemble contigs, extend sequences,
or error-correct reads. Tadpole has no upper bound for kmer length,
but some values are not supported. Specifically, it allows 1-31,
multiples of 2 from 32-62, multiples of 3 from 63-93, etc.
Please read bbmap/docs/guides/TadpoleGuide.txt for more information.
Usage:
Assembly: tadpole.sh in=<reads> out=<contigs>
Extension: tadpole.sh in=<reads> out=<extended> mode=extend
Correction: tadpole.sh in=<reads> out=<corrected> mode=correct
Extension and correction may be done simultaneously. Error correction on
multiple files may be done like this:
tadpole.sh in=libA_r1.fq,libA_merged.fq in2=libA_r2.fq,null extra=libB_r1.fq out=ecc_libA_r1.fq,ecc_libA_merged.fq out2=ecc_libA_r2.fq,null mode=correct
Extending contigs with reads could be done like this:
tadpole.sh in=contigs.fa out=extended.fa el=100 er=100 mode=extend extra=reads.fq k=62
Input parameters:
in=<file> Primary input file for reads to use as kmer data.
in2=<file> Second input file for paired data.
extra=<file> Extra files for use as kmer data, but not for error-
correction or extension.
reads=-1 Only process this number of reads, then quit (-1 means all).
NOTE: in, in2, and extra may also be comma-delimited lists of files.
Output parameters:
out=<file> Write contigs (in contig mode) or corrected/extended
reads (in other modes).
out2=<file> Second output file for paired output.
outd=<file> Write discarded reads, if using junk-removal flags.
dot=<file> Write a contigs connectivity graph (partially implemented)
dump=<file> Write kmers and their counts.
fastadump=t Write kmers and counts as fasta versus 2-column tsv.
mincounttodump=1 Only dump kmers with at least this depth.
showstats=t Print assembly statistics after writing contigs.
Prefiltering parameters:
prefilter=0 If set to a positive integer, use a countmin sketch
to ignore kmers with depth of that value or lower.
prehashes=2 Number of hashes for prefilter.
prefiltersize=0.2 (pff) Fraction of memory to use for prefilter.
minprobprefilter=t (mpp) Use minprob for the prefilter.
prepasses=1 Use this many prefiltering passes; higher be more thorough
if the filter is very full. Set to 'auto' to iteratively
prefilter until the remaining kmers will fit in memory.
onepass=f If true, prefilter will be generated in same pass as kmer
counts. Much faster but counts will be lower, by up to
prefilter's depth limit.
Hashing parameters:
k=31 Kmer length (1 to infinity). Memory use increases with K.
prealloc=t Pre-allocate memory rather than dynamically growing;
faster and more memory-efficient. A float fraction (0-1)
may be specified; default is 1.
minprob=0.5 Ignore kmers with overall probability of correctness below this.
minprobmain=t (mpm) Use minprob for the primary kmer counts.
threads=X Spawn X hashing threads (default is number of logical processors).
rcomp=t Store and count each kmer together and its reverse-complement.
coremask=t All kmer extensions share the same hashcode.
fillfast=t Speed up kmer extension lookups.
Assembly parameters:
mincountseed=3 (mcs) Minimum kmer count to seed a new contig or begin extension.
mincountextend=2 (mce) Minimum kmer count continue extension of a read or contig.
It is recommended that mce=1 for low-depth metagenomes.
mincountretain=0 (mincr) Discard kmers with count below this.
maxcountretain=INF (maxcr) Discard kmers with count above this.
branchmult1=20 (bm1) Min ratio of 1st to 2nd-greatest path depth at high depth.
branchmult2=3 (bm2) Min ratio of 1st to 2nd-greatest path depth at low depth.
branchlower=3 (blc) Max value of 2nd-greatest path depth to be considered low.
minextension=2 (mine) Do not keep contigs that did not extend at least this much.
mincontig=auto (minc) Do not write contigs shorter than this.
mincoverage=1 (mincov) Do not write contigs with average coverage below this.
trimends=0 (trim) Trim contig ends by this much. Trimming by K/2
may yield more accurate genome size estimation.
contigpasses=16 Build contigs with decreasing seed depth for this many iterations.
contigpassmult=1.7 Ratio between seed depth of two iterations.
ownership=auto For concurrency; do not touch.
processcontigs=f Explore the contig connectivity graph. (partially implemented)
Processing modes:
mode=contig contig: Make contigs from kmers.
extend: Extend sequences to be longer, and optionally
perform error correction.
correct: Error correct only.
insert: Measure insert sizes.
discard: Discard low-depth reads, without error correction.
Extension parameters:
extendleft=100 (el) Extend to the left by at most this many bases.
extendright=100 (er) Extend to the right by at most this many bases.
ibb=t (ignorebackbranches) Do not stop at backward branches.
extendrollback=3 Trim a random number of bases, up to this many, on reads
that extend only partially. This prevents the creation
of sharp coverage discontinuities at branches.
Error-correction parameters:
ecc=f Error correct via kmer counts.
reassemble=t If ecc is enabled, use the reassemble algorithm.
pincer=f If ecc is enabled, use the pincer algorithm.
tail=f If ecc is enabled, use the tail algorithm.
eccfull=f If ecc is enabled, use tail over the entire read.
aggressive=f (aecc) Use aggressive error correction settings.
Overrides some other flags like errormult1 and deadzone.
conservative=f (cecc) Use conservative error correction settings.
Overrides some other flags like errormult1 and deadzone.
rollback=t Undo changes to reads that have lower coverage for
any kmer after correction.
markbadbases=0 (mbb) Any base fully covered by kmers with count below
this will have its quality reduced.
markdeltaonly=t (mdo) Only mark bad bases adjacent to good bases.
meo=t (markerrorreadsonly) Only mark bad bases in reads
containing errors.
markquality=0 (mq) Set quality scores for marked bases to this.
A level of 0 will also convert the base to an N.
errormult1=16 (em1) Min ratio between kmer depths to call an error.
errormult2=2.6 (em2) Alternate ratio between low-depth kmers.
errorlowerconst=3 (elc) Use mult2 when the lower kmer is at most this deep.
mincountcorrect=3 (mcc) Don't correct to kmers with count under this.
pathsimilarityfraction=0.45(psf) Max difference ratio considered similar.
Controls whether a path appears to be continuous.
pathsimilarityconstant=3 (psc) Absolute differences below this are ignored.
errorextensionreassemble=5 (eer) Verify this many kmers before the error as
having similar depth, for reassemble.
errorextensionpincer=5 (eep) Verify this many additional bases after the
error as matching current bases, for pincer.
errorextensiontail=9 (eet) Verify additional bases before and after
the error as matching current bases, for tail.
deadzone=0 (dz) Do not try to correct bases within this distance of
read ends.
window=12 (w) Length of window to use in reassemble mode.
windowcount=6 (wc) If more than this many errors are found within a
a window, halt correction in that direction.
qualsum=80 (qs) If the sum of the qualities of corrected bases within
a window exceeds this, halt correction in that direction.
rbi=t (requirebidirectional) Require agreement from both
directions when correcting errors in the middle part of
the read using the reassemble algorithm.
errorpath=1 (ep) For debugging purposes.
Junk-removal parameters (to only remove junk, set mode=discard):
tossjunk=f Remove reads that cannot be used for assembly.
This means they have no kmers above depth 1 (2 for paired
reads) and the outermost kmers cannot be extended.
Pairs are removed only if both reads fail.
tossdepth=-1 Remove reads containing kmers at or below this depth.
Pairs are removed if either read fails.
lowdepthfraction=0 (ldf) Require at least this fraction of kmers to be
low-depth to discard a read; range 0-1. 0 still
requires at least 1 low-depth kmer.
requirebothbad=f (rbb) Only discard pairs if both reads are low-depth.
tossuncorrectable (tu) Discard reads containing uncorrectable errors.
Requires error-correction to be enabled.
Shaving parameters:
shave=t Remove dead ends (aka hair).
rinse=t Remove bubbles.
wash= Set shave and rinse at the same time.
maxshavedepth=1 (msd) Shave or rinse kmers at most this deep.
exploredist=300 (sed) Quit after exploring this far.
discardlength=150 (sdl) Discard shavings up to this long.
Note: Shave and rinse can produce substantially better assemblies
for low-depth data, but they are very slow for large metagenomes.
Overlap parameters (for overlapping paired-end reads only):
merge=f Attempt to merge overlapping reads prior to
kmer-counting, and again prior to correction. Output
will still be unmerged pairs.
ecco=f Error correct via overlap, but do not merge reads.
testmerge=t Test kmer counts around the read merge junctions. If
it appears that the merge created new errors, undo it.
Java Parameters:
-Xmx This will be passed to Java to set memory usage, overriding the program's automatic memory detection.
-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.
