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Fig. 1 | BMC Research Notes

Fig. 1

From: Intronomics-MIP: a snakemake pipeline for analyzing multilocus intron polymorphisms in species identification and population genomics

Fig. 1

Flow diagram of the Intronomic-MIP pipeline from preprocessing to haplotype generation. Raw fastq reads processing: Cutadapt is used to demultiplex based on loci primers, discard low-quality bases, and remove adapters, setting a quality cutoff. Merging paired-end reads: FLASH merges pair-end reads, discarding loci where merged reads are < 10% of total. Reconstructing MIPs genotypes: SeekDeep pipeline clusters allelic variants, estimates allele frequencies with the qluster package, and filters out low-frequency alleles with processClusters. The final output retains only the top alleles by frequency for each locus and sample, with a cumulative fixed abundance

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BMC Research Notes

ISSN: 1756-0500

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