Ultra Model Sets 40 Al 50
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Ultra Model Sets 40 Al 50
study conducted in 2017 during which 4,856 reads were generated. all reads were mapped to the reference human genome (ref. 20 ) with bwa-mem and variants identified using freebayes. for this work, a subset of the reads was used. references 1. bengtsson s, philipp t, stenman m, berg i, knudsen k, ivansson m, et al. (2010) indications from a whole-genome sequence analysis of four individuals that a single ancient human survived the lgm in a southern swedish population. plos genet. 6(12):e1001048. https://doi.org/10.1371/journal.pgen.1001048 2. stolzenburg j, french j, reich w, lukaszewicz f, bull r, hollinger g, et al. (2017) nanopore sequencing of a neandertal genome. science. 355(6325):5865.1126/science.aan2653 3. trapnell c, hollister j, anders s, merriman r, pääbo s. (2014) variantcaller: an integrated haplotype caller in the samtools package. bioinformatics. 30(14):264724.1093/bioinformatics/btt188 4. artan m, ragoczy j, taylor r, phan n, blekhman s, du p, et al. (2017) genomes of three ancient medieval individuals from the island of crete. 355(6325):705.aal2484 5. alm j, karvonen t, siitonen o, tommela t, tarkka t, haarala m, et al. (2018) genome sequences of two medieval finns. nature. 561(7738):4369.1038/s41586-018-0375-9 6. seetharam s, mirnics j, vrana k, szidat p, cools r, dukes a, et al. (2016) archaeogenetics of ancient dna.
mitochondrial assembly a was produced using long-read data mapped to a combined assembly of the human mitochondrial genome sequence assembled by zhang et al. the new assembly was performed using another version of midas 55 with parameters in midas::bigd set to true and the rms ploidy set to 1 and a custom ploidy model was generated from the h.sapiens data set with all human data filtered out. variants were identified using freebayes v1.0.2 (ref. 57 ), a widely used method originally developed for short-read sequencing but also applicable to long reads, with the command:freebayes -c 2 -0 -o -q 20 -z 0.10 -e 0 -x -u -p 2 -f 0.6 -b alignments.bam -v asm.bayes.vcf -f asm.fasta 3d9ccd7d82
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