how to split paired-end fastq by barcode from smart-seq2

Question

[17318598206]

i have a pooled fastq, it is paired-end sequencing, i wan to split fastq by barcode,which soft should i choose? thank you

Answer 1

[Divon]

You can use my Genozip tool:

genozip myfile.fq.gz --fast
genocat --grep-w TTAGGC myfile.fq.genozip  # output all reads with the barcode TTAGGC

If you also want to also properly compress the fastq file (1.5-2X better than gz) while you're at it, replace the first command with:

genozip myfile-R1.fq.gz myfile-R2.fq.gz --pair --reference hs37d5.ref.genozip

Where the reference file is generated from any FASTA reference genome of the species with eg:

genozip --make-reference hs37d5.fa

See here: https://genozip.com

Paper: https://www.researchgate.net/publication/349347156_Genozip_-_A_Universal_Extensible_Genomic_Data_Compressor