two types of reads in Oxford nanopore data

[shakti83kumar]

Hi Sir
I have minION generated fastq file using flowcell 9.4.1. I preprocessed QC and adapter removal by fastplong tool and converted into fasta format. During analysis of fasta file, I came to know there are two types of reads.

The most of reads are like below format.
">"<read_id>
SEQUENCE

Few reads have mentioned as below
">"split-by-adapter-left-<read_id>
SEQUENCE
">"split-by-adapter-right-<read_id>
SEQUENCE
where read_id is same

I am wandering why two types of data is produced by ONT

Thanks & Regards
Shakti Kumar
SGPGIMS, Lucknow
UP India

few reads as example are mentioned below

split-by-adapter-left-f6b34cfc-e23b-4292-b87a-169db8bd2a6f runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=234 start_time=2025-01-15T15:13:23.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=f6b34cfc-e23b-4292-b87a-169db8bd2a6f basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4
GTTACGACTTCACCCCAATCATCTATCCCACCTTAGGCGGCTGGCTCCTTACGATTTACCTCACCGACTTCGGGTGTTACAAGCTCTCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGACTTCATGTGAAGCGAGTTGCAGCCTACAATCCGAACCTGAGACTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAGCCATTGTAGCACGTGTGTAGCCCAGGTCATGAGGGCATGATGATTTGACATCATCCCCACCTTCCTCCGGTTTATTACCCGGCAGTCGCTAGAGTGCCCAACTGAATGATGGCAATAACAATAGGGGTTGCGCTCGTTGCAGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCATGCACCACCTGTCACCTCTGTCCCGAAGGAAATCTCTATCTCTAGAGAGGTCAGAGGGATGTCAAGACAGTGAGTTCTTCGCGTTGCTTCAGGGTCTAAACCTTAATACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCATTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCGGCACTAAACCCCCGGAAAGGTCTAACACCTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCCACGCTTTCGAGCCTCCCAGCGTCAGTTACAAGCCAAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTCTTGCACTCCAAGTTAAACAGTTTCCAAAGCGTACTATGGTTAAGCCACAGCCTTTAACTTCAGAACATCTAACCGCCTGCGCTCGCTTTTACGCCCAATAAATCCGGACAACGCTCGGGGCCTACGTATTACTGCGGCTGCTGGCACGTAGTTAACCGTCCCTTTCTGGTAAGATACCGTCACAGTGTGAACTTTCCACTCTCACACTCGTTCTTCTCTTACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGTTGCTCCGTTCAGACTTCAATCCATTGCCGAAGATTCCCTACTGCTGCCTCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCCCAGGTCGGCTATGTATCGTCGCCTTGGTGAGCCGTTACCGCCAACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAATTGCACCTTTTAAGCAAATGTCATGCAACATCTACTGTTATGCGGTATTAGCTATCGTTTCAATAGTTATCCCCCGCTACCAGGCAGGTTACCTACGCGTTACTCACCCGTTCACCCAACTCATCCAGAGAAGCAAGCTCCTCCTTCAGCGTTCTACTTGCATGTATTAGGCACGCCGCCAGCGTTCGTCCTGAGCCATG
split-by-adapter-right-f6b34cfc-e23b-4292-b87a-169db8bd2a6f runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=234 start_time=2025-01-15T15:13:23.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=f6b34cfc-e23b-4292-b87a-169db8bd2a6f basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4
TCAATTGTGCTTCCATTTCAGTTTCTAATTGGGTGTTTATGGACCGCCATACTACCGTGACGTTCATCTATCGGAGGAATGGACGGTTACCTTGTTACGACTTCCCACCCCAATCATCTATCCCACCTTCGACGGCTCCCTCCTATAAGGTTAGGCCACCGGCTTCGGGTGTTACAAACTCTCGTGGTGTGACGGGCGAGGGTGTGGCCGCAAGACCGGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGGCTTCATGTAGTCGAGTTGCAGACTACAATCCGAACCGAGAATGGCTTTTAGAGATTCGCTTACCCTCGCGAGTTCGCTGCTCGTTGTACCATCCATTGTAGCACGTGTGTAGCCCAGGTCATAAGGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCTTCAAGGTCCCCCATCTCAATGCTGGCAACTAGTTATAGGGGTTTGCGCTCGTTGCAGGACTTAACCCAACATCTCCACGACACGAGCTGACGACAACCACATGCACCACCTGTCACCGACGTTCCGAAGAAAAAACTCTATCTCTAGAGCGGTCGTCGGGATGTCAAGACCTGAAAGCTAAGGTTCTTCGCGTTGCTTCGAATTAAACCCACATGTGCTCCACCGCTTGTGCGGTCCCCGTCAATTCCTTTGAGGTTTCAGCCTTGCGGCCGTACTCCCCAGGCGGAGTGCTTGTGCGTTAACTCCAGCACTGAAGGTGGAACCCCTCCAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGAGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGGCCGCCTTCGCCACTGGTGTTCTCCATATATCTACGCATTTCCACACCGCTACACATGGAAATTCCGCTCTCCTCTTCCTGCCTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAAGACCGCTTCCACTCCCT

081dc771-22b4-4381-ab43-48ef7d419074 runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=67 start_time=2025-01-15T15:13:24.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=081dc771-22b4-4381-ab43-48ef7d419074 basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4 TACGACTTCACCCCAATCATCTATCCCACCTTAGGCGGCTGGCTCCTAAAGGTTACCCCTCACCGACTTCCGGGTGTTACAAACTCTCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGACTGGCTTTAAGAGATTAGCAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAGCCATTGTAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGAAGCGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAAAATTGCCCAACTAAAATGAGCAACTATGCAACTAACAATAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACTACAGCCACATGCACCACCTGTCACCTCTGTCCCGAAGGAAAACTCTATCTCTAGAGCGGTCAGAGGGATGTCAAAGACCTATTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGAGCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATACGTGCTTGCGGCACTAAACCCCGGAAAGGGTCTAACACCTAGCACTCATCGTTTACGGCACGTGGACTACCAGGGTATCTAATCCTGTTGCTCCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAAACCAGGGAAACCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACAGCGGAATTCCACTCTCCCCTCTTGCACTCAAGTTAAACGGTTTCAAAGCGTACTATGGTTAAGCCACAGCCTTTAACTTCAGACTTATCTAACCGCCTGCACTCGCCTTATCAATCCGGACAACGCTCGGGACCCTGCAGCCCCCACCGCGGCCGGCGGCGCTGGTGGCCGTCCCTTTCTGGTAAGATGCCGTCACAGTGTGAACTTTCCACTCTCACACTCGTTCTTCTCTTACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGTTGCTCCCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTTGCCTTGGTGAGCCGTTACCCCGCAACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAATTGCACCTTTTAATTGACTATCATGCAATAATCGGTATGCAGTATTAGCTATCGTTTCCAATAGTTATCCCCCGCTACCAGGCAGGTTACCTACGCGTTACTCACCCGTTCACCAACTCATCCAGAGAAACAAGCTCTCCTTCAGCGTTCTCTACTTGCATGTATTGAGCACCACCAGCGTTCGTCCTGAGCCATGA

Example are mentioned below

split-by-adapter-left-f6b34cfc-e23b-4292-b87a-169db8bd2a6f runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=234 start_time=2025-01-15T15:13:23.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=f6b34cfc-e23b-4292-b87a-169db8bd2a6f basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4
GTTACGACTTCACCCCAATCATCTATCCCACCTTAGGCGGCTGGCTCCTTACGATTTACCTCACCGACTTCGGGTGTTACAAGCTCTCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGACTTCATGTGAAGCGAGTTGCAGCCTACAATCCGAACCTGAGACTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAGCCATTGTAGCACGTGTGTAGCCCAGGTCATGAGGGCATGATGATTTGACATCATCCCCACCTTCCTCCGGTTTATTACCCGGCAGTCGCTAGAGTGCCCAACTGAATGATGGCAATAACAATAGGGGTTGCGCTCGTTGCAGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCATGCACCACCTGTCACCTCTGTCCCGAAGGAAATCTCTATCTCTAGAGAGGTCAGAGGGATGTCAAGACAGTGAGTTCTTCGCGTTGCTTCAGGGTCTAAACCTTAATACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCATTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCGGCACTAAACCCCCGGAAAGGTCTAACACCTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCCACGCTTTCGAGCCTCCCAGCGTCAGTTACAAGCCAAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTCTTGCACTCCAAGTTAAACAGTTTCCAAAGCGTACTATGGTTAAGCCACAGCCTTTAACTTCAGAACATCTAACCGCCTGCGCTCGCTTTTACGCCCAATAAATCCGGACAACGCTCGGGGCCTACGTATTACTGCGGCTGCTGGCACGTAGTTAACCGTCCCTTTCTGGTAAGATACCGTCACAGTGTGAACTTTCCACTCTCACACTCGTTCTTCTCTTACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGTTGCTCCGTTCAGACTTCAATCCATTGCCGAAGATTCCCTACTGCTGCCTCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCCCAGGTCGGCTATGTATCGTCGCCTTGGTGAGCCGTTACCGCCAACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAATTGCACCTTTTAAGCAAATGTCATGCAACATCTACTGTTATGCGGTATTAGCTATCGTTTCAATAGTTATCCCCCGCTACCAGGCAGGTTACCTACGCGTTACTCACCCGTTCACCCAACTCATCCAGAGAAGCAAGCTCCTCCTTCAGCGTTCTACTTGCATGTATTAGGCACGCCGCCAGCGTTCGTCCTGAGCCATG
split-by-adapter-right-f6b34cfc-e23b-4292-b87a-169db8bd2a6f runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=234 start_time=2025-01-15T15:13:23.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=f6b34cfc-e23b-4292-b87a-169db8bd2a6f basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4
TCAATTGTGCTTCCATTTCAGTTTCTAATTGGGTGTTTATGGACCGCCATACTACCGTGACGTTCATCTATCGGAGGAATGGACGGTTACCTTGTTACGACTTCCCACCCCAATCATCTATCCCACCTTCGACGGCTCCCTCCTATAAGGTTAGGCCACCGGCTTCGGGTGTTACAAACTCTCGTGGTGTGACGGGCGAGGGTGTGGCCGCAAGACCGGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGGCTTCATGTAGTCGAGTTGCAGACTACAATCCGAACCGAGAATGGCTTTTAGAGATTCGCTTACCCTCGCGAGTTCGCTGCTCGTTGTACCATCCATTGTAGCACGTGTGTAGCCCAGGTCATAAGGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCTTCAAGGTCCCCCATCTCAATGCTGGCAACTAGTTATAGGGGTTTGCGCTCGTTGCAGGACTTAACCCAACATCTCCACGACACGAGCTGACGACAACCACATGCACCACCTGTCACCGACGTTCCGAAGAAAAAACTCTATCTCTAGAGCGGTCGTCGGGATGTCAAGACCTGAAAGCTAAGGTTCTTCGCGTTGCTTCGAATTAAACCCACATGTGCTCCACCGCTTGTGCGGTCCCCGTCAATTCCTTTGAGGTTTCAGCCTTGCGGCCGTACTCCCCAGGCGGAGTGCTTGTGCGTTAACTCCAGCACTGAAGGTGGAACCCCTCCAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGAGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGGCCGCCTTCGCCACTGGTGTTCTCCATATATCTACGCATTTCCACACCGCTACACATGGAAATTCCGCTCTCCTCTTCCTGCCTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAAGACCGCTTCCACTCCCT

081dc771-22b4-4381-ab43-48ef7d419074 runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=67 start_time=2025-01-15T15:13:24.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=081dc771-22b4-4381-ab43-48ef7d419074 basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4
TACGACTTCACCCCAATCATCTATCCCACCTTAGGCGGCTGGCTCCTAAAGGTTACCCCTCACCGACTTCCGGGTGTTACAAACTCTCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGACTGGCTTTAAGAGATTAGCAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAGCCATTGTAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGAAGCGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAAAATTGCCCAACTAAAATGAGCAACTATGCAACTAACAATAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACTACAGCCACATGCACCACCTGTCACCTCTGTCCCGAAGGAAAACTCTATCTCTAGAGCGGTCAGAGGGATGTCAAAGACCTATTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGAGCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATACGTGCTTGCGGCACTAAACCCCGGAAAGGGTCTAACACCTAGCACTCATCGTTTACGGCACGTGGACTACCAGGGTATCTAATCCTGTTGCTCCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAAACCAGGGAAACCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACAGCGGAATTCCACTCTCCCCTCTTGCACTCAAGTTAAACGGTTTCAAAGCGTACTATGGTTAAGCCACAGCCTTTAACTTCAGACTTATCTAACCGCCTGCACTCGCCTTATCAATCCGGACAACGCTCGGGACCCTGCAGCCCCCACCGCGGCCGGCGGCGCTGGTGGCCGTCCCTTTCTGGTAAGATGCCGTCACAGTGTGAACTTTCCACTCTCACACTCGTTCTTCTCTTACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGTTGCTCCCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTTGCCTTGGTGAGCCGTTACCCCGCAACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAATTGCACCTTTTAATTGACTATCATGCAATAATCGGTATGCAGTATTAGCTATCGTTTCCAATAGTTATCCCCCGCTACCAGGCAGGTTACCTACGCGTTACTCACCCGTTCACCAACTCATCCAGAGAAACAAGCTCTCCTTCAGCGTTCTCTACTTGCATGTATTGAGCACCACCAGCGTTCGTCCTGAGCCATGA

081dc771-22b4-4381-ab43-48ef7d419074 runid=cf356292e48ca53dc990f616273889d27d7fd890 ch=67 start_time=2025-01-15T15:13:24.246766+05:30 flow_cell_id=FAY87352 protocol_group_id=Metagenomics1 sample_id= barcode=barcode01 barcode_alias=barcode01 parent_read_id=081dc771-22b4-4381-ab43-48ef7d419074 basecall_model_version_id=dna_r9.4.1_e8_fast@v3.4
TACGACTTCACCCCAATCATCTATCCCACCTTAGGCGGCTGGCTCCTAAAGGTTACCCCTCACCGACTTCCGGGTGTTACAAACTCTCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGACTGGCTTTAAGAGATTAGCAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAGCCATTGTAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGAAGCGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAAAATTGCCCAACTAAAATGAGCAACTATGCAACTAACAATAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACTACAGCCACATGCACCACCTGTCACCTCTGTCCCGAAGGAAAACTCTATCTCTAGAGCGGTCAGAGGGATGTCAAAGACCTATTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGAGCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATACGTGCTTGCGGCACTAAACCCCGGAAAGGGTCTAACACCTAGCACTCATCGTTTACGGCACGTGGACTACCAGGGTATCTAATCCTGTTGCTCCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAAACCAGGGAAACCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACAGCGGAATTCCACTCTCCCCTCTTGCACTCAAGTTAAACGGTTTCAAAGCGTACTATGGTTAAGCCACAGCCTTTAACTTCAGACTTATCTAACCGCCTGCACTCGCCTTATCAATCCGGACAACGCTCGGGACCCTGCAGCCCCCACCGCGGCCGGCGGCGCTGGTGGCCGTCCCTTTCTGGTAAGATGCCGTCACAGTGTGAACTTTCCACTCTCACACTCGTTCTTCTCTTACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGTTGCTCCCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTTGCCTTGGTGAGCCGTTACCCCGCAACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAATTGCACCTTTTAATTGACTATCATGCAATAATCGGTATGCAGTATTAGCTATCGTTTCCAATAGTTATCCCCCGCTACCAGGCAGGTTACCTACGCGTTACTCACCCGTTCACCAACTCATCCAGAGAAACAAGCTCTCCTTCAGCGTTCTCTACTTGCATGTATTGAGCACCACCAGCGTTCGTCCTGAGCCATGA