fastq文件排序对比对率的影响：seqkit 安装和使用

conda install -c bioconda seqkit

sort sequences by id/name/sequence/length.

By default, all records will be readed into memory.
For FASTA format, use flag -2 (--two-pass) to reduce memory usage. FASTQ not
supported.

Firstly, seqkit reads the sequence head and length information.
If the file is not plain FASTA file,
seqkit will write the sequences to temporary files, and create FASTA index.

Secondly, seqkit sorts sequence by head and length information
and extracts sequences by FASTA index.

Usage:
  seqkit sort [flags]

Flags:
  -b, --by-bases                by non-gap bases
  -l, --by-length               by sequence length
  -n, --by-name                 by full name instead of just id
  -s, --by-seq                  by sequence
  -G, --gap-letters string      gap letters (default "- \t.")
  -h, --help                    help for sort
  -i, --ignore-case             ignore case
  -k, --keep-temp               keep temporary FASTA and .fai file when using 2-pass mode
  -N, --natural-order           sort in natural order, when sorting by IDs/full name
  -r, --reverse                 reverse the result
  -L, --seq-prefix-length int   length of sequence prefix on which seqkit sorts by sequences (0 for whole sequence) (default 10000)
  -2, --two-pass                two-pass mode read files twice to lower memory usage. (only for FASTA format)

Global Flags:
      --alphabet-guess-seq-length int   length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq) (default 10000)
      --id-ncbi                         FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...
      --id-regexp string                regular expression for parsing ID (default "^(\\S+)\\s?")
      --infile-list string              file of input files list (one file per line), if given, they are appended to files from cli arguments
  -w, --line-width int                  line width when outputting FASTA format (0 for no wrap) (default 60)
  -o, --out-file string                 out file ("-" for stdout, suffix .gz for gzipped out) (default "-")
      --quiet                           be quiet and do not show extra information
  -t, --seq-type string                 sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence) (default "auto")
  -j, --threads int                     number of CPUs. can also set with environment variable SEQKIT_THREADS) (default 4)

Time loading forward index: 00:00:22
Time loading reference: 00:00:03
Multiseed full-index search: 00:11:30
23576060 reads; of these:
  23576060 (100.00%) were paired; of these:
    1398071 (5.93%) aligned concordantly 0 times
    21068790 (89.37%) aligned concordantly exactly 1 time
    1109199 (4.70%) aligned concordantly >1 times
    ----
    1398071 pairs aligned concordantly 0 times; of these:
      39078 (2.80%) aligned discordantly 1 time
    ----
    1358993 pairs aligned 0 times concordantly or discordantly; of these:
      2717986 mates make up the pairs; of these:
        1728911 (63.61%) aligned 0 times
        892790 (32.85%) aligned exactly 1 time
        96285 (3.54%) aligned >1 times
96.33% overall alignment rate
Time searching: 00:11:34
Overall time: 00:11:56

Time loading forward index: 00:00:25
Time loading reference: 00:00:04
Multiseed full-index search: 00:08:33
23576060 reads; of these:
  23576060 (100.00%) were paired; of these:
    1390031 (5.90%) aligned concordantly 0 times
    21078357 (89.41%) aligned concordantly exactly 1 time
    1107672 (4.70%) aligned concordantly >1 times
    ----
    1390031 pairs aligned concordantly 0 times; of these:
      39187 (2.82%) aligned discordantly 1 time
    ----
    1350844 pairs aligned 0 times concordantly or discordantly; of these:
      2701688 mates make up the pairs; of these:
        1717885 (63.59%) aligned 0 times
        890091 (32.95%) aligned exactly 1 time
        93712 (3.47%) aligned >1 times
96.36% overall alignment rate
Time searching: 00:08:37
Overall time: 00:09:02