MIRAbait: 256bpまでのkmerのための「grep」のようなツール
mirabaitは、リードコレクションの中から、ターゲットベイトとして定義された配列と部分的に類似した、あるいは等しいリードを選択する。類似性とは、ベイト配列と選択されるスクリーニング配列の間に、ユーザーが調整可能な数の共通のk-mer（k個の連続した塩基からなる配列）を見つけることで定義される（順方向または順逆相補方向）。4塩基までのリピートに対して、DUSTのようなリピートフィルターを追加することもできる。ペアエンドファイルで使用した場合、少なくとも1つのメイトが一致する配列を選ぶ。
インストール
V5rc1をダウンロードしてパスを通した（ubuntu18.04使用)。v4はcondaで導入できます。
最新版のバイナリ（V5rc1）
#version4
mamba create -n mira -y
conda activate mira
mamba install -c bioconda mira -y
> mirabait
$ mirabait
# ./mirabait
Usage: mirabait [options] {-b baitfile [-b ...] | -B file | -j joblibrary} {-p file_1 file_2 | -P file3}* [file4 ...]
MIRAbait: a 'grep' like tool for kmers up to 256 bp
mirabait selects reads from a read collection which are partly similar or
equal to sequences defined as target baits. Similarity is defined by finding a
user-adjustable number of common k-mers (sequences of k consecutive bases)
which are the same in the bait sequences and the screened sequences to be
selected, either in forward or forward/reverse complement direction. Adding a
DUST-like repeat filter for repeats up 4 bases is optional.
When used on paired files, selects sequences where at least one mate matches.
Options:
-b file Load bait sequences from file
(multiple -b allowed)
-B file Load baits from kmer statistics file, not from sequence files.
Only one -B allowed, cannot be combined with -b.
(see -K for creating such a file)
-j job Set options for predefined job from supplied MIRA library
Currently available jobs:
rrna Bait rRNA sequences
-p file1 file2 Load paired sequences to search from file1 and file2
Files must contain same number of sequences, sequence
names must be in same order.
Multiple -p allowed, but must come before non-paired
files.
-P file Load paired sequences from file
File must be interleaved: pairs must follow each other,
non-pairs are not allowed.
Multiple -p allowed, but must come before non-paired
files.
-k int kmer length of bait in bases (<=256, default=31)
-n int If >0: minimum number of k-mer baits needed (default=1)
If <=0: allowed number of missed kmers over sequence
length
-d Do not use kmers with microrepeats (DUST-like, see also -D)
-D int Set length of microrepeats in kmers to discard from bait.
int > 0 microrepeat len in percentage of kmer length.
E.g.: -k 17 -D 67 --> 11.39 bases --> 12 bases.
int < 0 microrepeat len in bases.
int != 0 implies -d, int=0 turns DUST filter off.
-i Selects sequences that do not hit bait
-I Selects sequences that hit and do not hit bait (to
different files)
-r No checking of reverse complement direction
-t Number of threads to use (default=0 -> up to 4 CPU cores)
Options for output definition:
Normally mirabait writes separate result files (named 'bait_match_*' and
'bait_miss_*') for each input to the current directory. For changing this
behaviour and other relating to output, use these options:
-c char Normally, mirabait lowercases bases a kmer hit.
Using this option, one can instead mask those bases with the
given character.
Use a blank to neither mask nor lowercase hits.
-l int length of a line (FASTA only, default 0=unlimited)
-K file Save kmer statistics to 'file' (see also -B)
-N name Change the prefix 'bait' to <name>
Has no effect if -o/-O is used and targets are not
directories
-o <path> Save sequences matching bait to path
If path is a directory, write separate files into this
directory. If not, combine all matching sequences from
the input file(s) into a single file specified by the
path.
-O <path> Like -o, but for sequences not matching
Other options:
-T dir Use 'dir' as directory for temporary files instead of
current working directory.
-m integer Memory to use for computing kmer statistics
0..100 = use percentage of free system memory
>100 = amount of MiB to use (e.g. 16384 for 16 GiB)
Default 75 (75% of free system memory).
Defining files types to load/save:
Normally mirabait recognises the file types according to the file extension
(even when packed). In cases you need to force a certain file type because the
file extension is non-standard, use the EMBOSS notation to force a type:
<filetype>::<name_of_file>. E.g., to tell that "somefile.dat" is FASTQ, use:
fastq::somefile.dat
Recognised types are: caf, fasta, fastq, gbf, gbk, gbff, maf and phd.
MIRABAIT will write files in the same file type as the corresponding input
files.
Examples:
mirabait -b b.fasta file.fastq
mirabait -I -j rrna -p file_1.fastq file_2.fastq
mirabait -b b1.fasta -b b2.gbk file.fastq
mirabait -b fasta::baits.dat -p fastq::file_1.dat fastq::file_2.dat
mirabait -b b.fasta -p file_1.fastq file_2.fastq -P file3.fasta file4.caf
mirabait -I -b b.fasta -p file_1.fastq file_2.fastq -P file3.fasta file4.caf
mirabait -k 27 -n 10 -b b.fasta file.fastq
mirabait -b fasta::b.dat fastq::file.dat
mirabait -o /dev/shm/ -b b.fasta -p file_1.fastq file_2.fastq
mirabait -o /dev/shm/match -b b.fasta -p file_1.fastq file_2.fastq
mirabait -b human_genome.fasta -K HG_kmerstats.mhs.gz -p file1.fastq file2.fastq
mirabait -B HG_kmerstats.mhs.gz -p file1.fastq file2.fastq
mirabait -d -B HG_kmerstats.mhs.gz -p file1.fastq file2.fastq
./mirabait: No bait files defined via -b and no -B given!
Did you use the command line for the old mirabait (<= 4.0.2)?
実行方法
baitリファレンスとfastqファイル（.fastq）を指定する。gzip圧縮fastqには対応していない。
mirabait -b ref.fasta input.fastq
- -b <file> Load bait sequences from file (multiple -b allowed)
- -k <int> kmer length of bait in bases (<=256, default=31)-k int kmer length of bait in bases (<=256, default=31)
baitリファレンスとマッチしたリードが出力される。
ペアエンドfastq
mirabait -b ref.fasta -p pair_R1.fastq pair_R2.fastq
- -p <file1> <file2> Load paired sequences to search from file1 and file2. Files must contain same number of sequences, sequence names must be in same order. Multiple -p allowed, but must come before non-paired files.
- -P <file> Load paired sequences from file. File must be interleaved: pairs must follow each other, non-pairs are not allowed. Multiple -p allowed, but must come before non-paired files.
ペアエンドfastqは同期されたまま出力される。
”-i”をつけるとbait配列にヒットしないリードが出力される。
引用
Chevreux, B., Wetter, T. and Suhai, S. (1999): Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J., Müller, W. E., Wetter, T. and Suhai, S. (2004): Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome Research, 14(6)
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