sequences fastx_toolkit zcat -f '$input' | fastx_collapser -v -o '$output' **What it does** This tool collapses identical sequences in a FASTA file into a single sequence. -------- **Example** Example Input File (Sequence "ATAT" appears multiple times):: >CSHL_2_FC0042AGLLOO_1_1_605_414 TGCG >CSHL_2_FC0042AGLLOO_1_1_537_759 ATAT >CSHL_2_FC0042AGLLOO_1_1_774_520 TGGC >CSHL_2_FC0042AGLLOO_1_1_742_502 ATAT >CSHL_2_FC0042AGLLOO_1_1_781_514 TGAG >CSHL_2_FC0042AGLLOO_1_1_757_487 TTCA >CSHL_2_FC0042AGLLOO_1_1_903_769 ATAT >CSHL_2_FC0042AGLLOO_1_1_724_499 ATAT Example Output file:: >1-1 TGCG >2-4 ATAT >3-1 TGGC >4-1 TGAG >5-1 TTCA .. class:: infomark Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. The following output:: >2-4 ATAT means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.