minimap2和yacrd 去16S nanopore的嵌合体【学习笔记】

最新推荐文章于 2024-06-27 16:30:00 发布

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最新推荐文章于 2024-06-27 16:30:00 发布

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本文链接：https://blog.csdn.net/weixin_46623488/article/details/121868746

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WARNING:

Minimap2 v2.19 introduce some change in selection of seed and chaining of this seed to generate overlap. This change could have an important impacte on yacrd behavior, I can’t guarantee the quality of yacrd results with this version of minimap2, I recommend you not to use a minimap2 version higher than 2.18.

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cd到安装的目录，make安装软件，要打开软件cd到安装目录，在安装目录才可以操作

cd xxx/xxx/minimap2.18/     【打开软件方式】
./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf   【运行软件方式】

minimap2 -x {corresponding preset} reads.fq reads.fq > mapping.paf
yacrd -i mapping.paf -o reads.yacrd filter -i reads.fasta -o reads.filter.fasta
yacrd -i mapping.paf -o reads.yacrd extract -i reads.fasta -o reads.extract.fasta
yacrd -i mapping.paf -o reads.yacrd split -i reads.fasta -o reads.split.fasta
yacrd -i mapping.paf -o reads.yacrd scrubb -i reads.fasta -o reads.scrubb.fasta

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minimap2 -x ava-pb -g 5000 reads.fasta reads.fasta > overlap.paf
yacrd -i overlap.paf -o report.yacrd -c 4 -n 0.4 scrubb -i reads.fasta -o reads.scrubb.fasta

$yacrd -h
yacrd 0.6.2 Ivysaur
Pierre Marijon <pmarijon@mpi-inf.mpg.de>

Yacrd use overlap between reads, to detect 'good' and 'bad' region,
a region with coverage over the threshold is 'good' others are 'bad'.
If read has a 'bad' region in middle this reads is mark as 'Chimeric'.
If the ratio of 'bad' region length on total read length is larger than threshold this reads is mark
as 'Not_covered'.

Yacrd can make some other actions:
- filter: for sequence or overlap file, record with reads marked as Chimeric or NotCovered isn't
written in the output
- extract: for sequence or overlap file, record contains reads marked as Chimeric or NotCovered is
written in the output
- split: for sequence file bad region in the middle of reads are removed, NotCovered read is removed
- scrubb: for sequence file all bad region are removed, NotCovered read is removed

USAGE:
    yacrd [OPTIONS] --input <input> --output <output> [SUBCOMMAND]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -c, --coverage <coverage>
            if coverage reach this value region is mark as bad [default: 0]

    -i, --input <input>
            path to input file overlap (.paf|.m4|.mhap) or yacrd report (.yacrd), format is
            autodetect and compression input is allowed (gz|bzip2|lzma)

    -n, --not-coverage <not-coverage>
            if the ratio of bad region length on total length is lower than this value, read is
            marked as NotCovered [default: 0.8]

    -d, --ondisk <ondisk>
            yacrd switches to 'ondisk' mode which will reduce memory usage but increase computation
            time. The value passed as a parameter is used as a prefix for the temporary files
            created by yacrd. Be careful if the prefix contains path separators (`/` for unix or `\`
            for windows) this folder will be deleted

        --ondisk-buffer-size <ondisk-buffer-size>
            with the default value yacrd in 'ondisk' mode use around 1 GBytes, you can increase to
            reduce runtime but increase memory usage [default: 64000000]

    -o, --output <output>                            path output file

SUBCOMMANDS:
    extract    Record mark as chimeric or NotCovered is extract
    filter     Record mark as chimeric or NotCovered is filter
    help       Prints this message or the help of the given subcommand(s)
    scrubb     All bad region of read is removed
    split      Record mark as chimeric or NotCovered is split