Illumina Sequencing of Fecal Samples from Mucin 13 animals before and after stress
SCHLOSS primer designDevelopment of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on theMiSeq Illumina sequencing platform; Kozich et alhttps://www.ncbi.nlm.nih.gov/pubmed/23793624GENERIC PRIMER DESIGNAATGATACGGCGACCACCGAGATCTACAC <i5><pad><link><16Sf> VX.N5??CAAGCAGAAGACGGCATACGAGAT <i7><pad><link><16Sr> VX.N7??Generic read 1 primer design<pad><link><16Sf> VX.read1Generic read 2 primer design<pad><link><16Sr> VX.read2Generic index read primer designReverse complement of (<pad><link><16Sr>) VX.p7_index16SfV3: CCTACGGGAGGCAGCAGV4: GTGCCAGCMGCCGCGGTAA16SrV4: GGACTACHVGGGTWTCTAATV5: CCCGTCAATTCMTTTRAGTLink:V4f: GTV4r: CCV3f: GGV5r: GGPad:Forward: TATGGTAATTReverse: AGTCAGTCAGV4 Schloss primersi5Illumina i5 INDEX_________________________________ ________AATGATACGGCGACCACCGAGATCTACAC XXXXXXXX TATGGTAATT GT GTGCCAGCMGCCGCGGTAA___________ __ _______________________PAD LINK V4i7Illumina i7 INDEX____________________________ ________CAAGCAGAAGACGGCATACGAGAT XXXXXXXX AGTCAGTCAG CC GGACTACHVGGGTWTCTAAT___________ __ _______________________PAD LINK V4Read 1 primer for V4 region<PADLINKV4>TATGGTAATTGTGTGCCAGCMGCCGCGGTAARead 2 primer for V4 region<PADLINKV4>AGTCAGTCAGCCGGACTACHVGGGTWTCTAATIndex primer for V4 region<Reverse complement <V4LINKPAD>ATTAGAWACCCBDGTAGTCCGGCTGACTGACTV1-V3 Schloss primersi5Illumina i5 INDEX_________________________________ ________AATGATACGGCGACCACCGAGATCTACAC XXXXXXXX TATGGTAATT GT AGAGTTTGATCCTGGCTCAG___________ __ _______________________PAD LINK V1; 27Fi7Illumina i7 INDEX____________________________ ________CAAGCAGAAGACGGCATACGAGAT XXXXXXXX AGTCAGTCAG GG ATTACCGCGGCTGCTGG___________ __ ___________________PAD LINK V3; 534RRead 1 primer for V1 region<PADLINKV1>TATGGTAATTGTAGAGTTTGATCCTGGCTCAGRead 2 primer for V3 region<PADLINKV3>AGTCAGTCAGGGATTACCGCGGCTGCTGGIndex primer for V1-V3 region<Reverse complement <V3LINKPAD>CCAGCAGCCGCGGTAATCCCTGACTGACT