https://www.biostars.org/p/483594/より
bbmask.shはSTR（リピート長1-15bp）をマスクすることができ、findrepeats.shは様々なタイプの長いリピートや部分的なリピートを見つけて報告またはマスクすることができる。
インストール
いくつかのツールはcondaでダウンロードできるBBtoolsパッケージには含まれない。ソースコードをダウンロードして使用した。
cd bbmap/
chmod u+x ./*sh
>./findrepeats.sh
Written by Brian Bushnell
Last modified July 5, 2023
Description: Finds repeats in a genome.
No alignment is done; a sequence is considered to be a repeat of depth D if
all kmers within it have a depth of at least D. Gaps of up to length G
consecutive kmers with lower counts may be allowed, which typically finds
far more and substantially longer repeats even with a small G.
Usage: findrepeats.sh in=<input file> out=<output file>
Standard parameters:
in=<file> Primary input (the genome fasta).
out=<file> Primary output (list of repeats as TSV). If no file is
given this will be printed to screen; to suppress printing,
use 'out=null'.
outs=<file> (outsequence) Optional sequence output, for printing or
masking repeats.
overwrite=f (ow) False ('f') forces the program to abort rather than
overwrite an existing file.
showspeed=t (ss) Set to 'f' to suppress display of processing speed.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
Processing parameters:
k=31 Kmer length to use (range is 1-31; 31 is recommended).
gap=0 Maximum allowed gap length within a repeat, in kmers.
This allows inexact repeats. Note that a 1bp mismatch
will spawn a length K gap.
qhdist=0 Hamming distance within a kmer; allows inexact repeats.
Values above 0 become exponentially slower.
minrepeat=0 Minimum repeat length to report, in bases. Nothing shorter
than kmer length will be found regardless of this value.
mindepth=2 Ignore copy counts below mindepth.
maxdepth=-1 If positive, copy counts greater than this will be reported
as this number. This can greatly increase speed in rare
cases of thousand+ copy repeats.
preview=27 Print this many characters of the repeat per line. Set to 0
to suppress (may save memory).
mask=f Write sequence with masked repeats to 'outs'. Possible values:
f: Do not mask.
t: Mask (by default, 't' or 'true' are the same as 'soft').
soft: Convert masked bases to lower case.
hard: Convert masked bases to 'N'.
Other characters: Convert masked bases to that character.
print=t (printrepeats) Print repeat sequence to outs. 'print' and
'mask' are mutually exclusive so enabling one will disable
the other.
weak=f (weaksubsumes) Ignore repeats that are weakly subsumed by
other repeats. A repeat is subsumed if there is another repeat
with greater depth at the same coordinates. Since a 3-copy
repeat is also a 2-copy repeat, only the 3-copy repeat will be
reported. However, in the case that the 3-copy repeat is
inexact (has gaps) and the 2-copy repeat is perfect, both will
be reported when 'weak=f' as per default. If you set the
'weak=t' flag, only the highest-depth version will be reported
even if it has more gaps. In either case all 3 repeats would
be reported, but with 'weak=f' some copies would be reported
twice for the same coordinates, once as a depth-2 perfect
repeat and again as a depth-3 imperfect repeat.
Java Parameters:
-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.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
実行方法
ゲノム配列と出力を指定する。
./findrepeats.sh in=genome.fasta out=out.txt gap=2 k=31
- k=31 Kmer length to use (range is 1-31; 31 is recommended).
- gap=0 Maximum allowed gap length within a repeat, in kmers. This allows inexact repeats. Note that a 1bp mismatch will spawn a length K gap.
（１列目depth、２列目長さ、ポジション順ではないので注意）
細菌ゲノムで試したところ、短いリピートから長いリピート（rRNAオペロン）まで検出されていた。
リピート領域をソフトマスク（小文字でマスク）したゲノム配列をを出力。
./findrepeats.sh in=genome.fasta outs=masked_genome.fasta mask=soft
- mask=f Write sequence with masked repeats to 'outs'. Possible values:
f: Do not mask.
t: Mask (by default, 't' or 'true' are the same as 'soft').
soft: Convert masked bases to lower case.
hard: Convert masked bases to 'N'.
Other characters: Convert masked bases to that character.
引用
https://sourceforge.net/projects/bbmap/
関連
