What it does

Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:

@test-6/1
AGCTTGACGC
+
?.HCF@C>>F
@test-6/2
TGCGAAGACC
+
>2?A?A@@7?
@test-4/1
CTTGACGCTG
+
I@>3EFCG@C
@test-2/1
AGACCAAAAT
+
??><6E?IFC
@test-2/2
CTGGCGAATT
+
?=?*?A?<?@

This tool will remove the offending reads (test-4/1), leaving just the paired data.

@test-6/1
AGCTTGACGC
+
?.HCF@C>>F
@test-6/2
TGCGAAGACC
+
>2?A?A@@7?
@test-2/1
AGACCAAAAT
+
??><6E?IFC
@test-2/2
CTGGCGAATT
+
?=?*?A?<?@

Attribution

This Galaxy tool relies on the seqtk toolkit from lh3/seqtk, developed by Heng Li at the Broad Institute