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References

Tags: #pangenome 🏠 home


Documentation:

References: Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, 7.

Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w 1118 ; iso-2; iso-3. Fly 6, 80–92.

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008.

Garrison E, Guarracino A. 2023. Unbiased pangenome graphs. Bioinformatics 39, btac743.

Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Moses MN, Nobrega FL, Wu Y, Chen H, De Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW, Prins P. 2023. Building pangenome graphs. , Preprint at https://www.biorxiv.org/content/10.1101/2023.04.05.535718v1.

Hickey G, Heller D, Monlong J, Sibbesen JA, Sirén J, Eizenga J, Dawson ET, Garrison E, Novak AM, Paten B. 2020. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology 21, 35.

Pertea G, Pertea M. 2020. GFF Utilities: GffRead and GffCompare. F1000Research 9.

Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842.

Shen W, Le S, Li Y, Hu F. 2016. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE 11, e0163962.

Zhou X, Stephens M. 2012. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics 44, 821–824.