# TRF: Total number of sequences with repeats removed from file

**URL:** <https://forum.biobakery.org/t/trf-total-number-of-sequences-with-repeats-removed-from-file/6116>\
**Category:** KneadData\
**Created:** [October 24, 2023, 4:51pm UTC](https://forum.biobakery.org/t/trf-total-number-of-sequences-with-repeats-removed-from-file/6116 "2023-10-24T16:51:06Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![ebeirns](https://avatars.discourse-cdn.com/v4/letter/e/82dd89/32.png) [@ebeirns](https://forum.biobakery.org/u/ebeirns)\
**Post date:** [October 24, 2023, 4:51pm UTC](https://forum.biobakery.org/t/trf-total-number-of-sequences-with-repeats-removed-from-file/6116/1 "2023-10-24T16:51:06Z")

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Could someone please clarify something from the kneaddata log file? I’m using version 0.12.0 and I’m confused (and alarmed) at the number of reads/sequences removed from my metagenomic files by TRF.

Input 1&2 read count: 70,179,888  
Trimmed paid 1&2 read count: 65,368,820 (93% of input reads)  
Repeats removed 1 sequence count: 305,115 (0.43% of input reads)  
Repeats removed 2 sequence count: 308,169 (0.44% of input reads)

Despite this seemly huge drop in the number of reads/sequences, the file sizes of the trimmed.fq’s are only slightly bigger than the repeats.removed.fq’s.

So my questions are: is the count of sequences given from TRF the number of reads it has removed? Is there a big difference in meaning between reads and sequences? Does TRF only remove short reads, hence the file sizes remain similar despite the huge number of reads removed?