3 File Formats

Here we have described in detail the acquisition method and formats of the input files and the output files.

Input files

File1: k-mers file (.Fasta)

example:

>1
ATCCGCAGCAGCCATATCCACAACAACCA
>1
AACAACAAGAACAACTCCCACAACAACTC
>1
ACATCATTGGCAAGGTCCGGAGTGCAATG
>1
GGCAATCGCTTTGTGGCCAGATTATCGAC
>1
CCAACTCCGGCGCCAACGCCGAATGGCAC

File2: sequencing data (.Fastq or .Fastq.gz)

example:

@A00164:490:HWTCWDSXX:2:1101:14877:1235 1:N:0:GGCTATAG+GTCCATCA
TAGCAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAGCAGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFF:FFFFF,FFFFF,FFFFF,FF,FF,
@A00164:490:HWTCWDSXX:2:1101:9263:1251 1:N:0:GGCTATAG+GTCCATCA
TGGTGGTGGTGGTGGTGGTGGTGGTGGTGTTGGTGTTGCTGTTGCTGTAGTTGCTGCTGTTGTTGTTATTGTTGTTGTTGTTATTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FFF:FFF,FFF,
@A00164:490:HWTCWDSXX:2:1101:9254:1266 1:N:0:GGCTATAG+GTCCATCA
TGGTGGTGGTGGTGGTGGTGGTGGTGGTGTTGGTGTTGCTGTTGCTGTAGTTGCTGCTGTTGTTGTTATTGTTGTTGTTGTTATTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGGTGGTGG

Output Files

File1: All reads containing the input k-mer (.Fastq)

example:

@A00164:490:HWTCWDSXX:2:1102:24406:6997 1:N:0:GGCTATAG+GTCCCTCA
TCCCGATGCCCGGCCATCCACAACATTGTGCACGCCATCGTCGTTCAACAACAACATGTGGATAGAGGTTTCGGCCAGCCTCAACCACAACAGTTGGGCCAGGGAATGCCCATGCAGCCTCAATATCAATTGGGCCAGGGCTTTATCCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFF
@A00164:490:HWTCWDSXX:2:1102:24406:6997 1:N:0:GGCTATAG+GTCCCTCA
TCCCGATGCCCGGCCATCCACAACATTGTGCACGCCATCGTCGTTCAACAACAACATGTGGATAGAGGTTTCGGCCAGCCTCAACCACAACAGTTGGGCCAGGGAATGCCCATGCAGCCTCAATATCAATTGGGCCAGGGCTTTATCCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFF
    

File2: The counting of the occurrence frequency of k-mer (.txt)

example:

AAAAAAAACAACAACAACAACTATCGAGC   0
AAAAAAACAACAACAACAACTATCGAGCC   1
AAAAAAACACCCAACAACCACAACAAATC   0
AAAAAAATTCATTTCAGATGCAGCCAAAC   2
AAAAAACAACAACAACAACTATCGAGCCA   0
AAAAAACACCCAACAACCACAACAAATCC   10
AAAAAATAGGACAAGGGCAACAACCAGAA   0
AAAAAATAGGACAAGGGCAACAACCAGGA   0