High-quality chromosome-scale de novo assembly of the Paspalum notatum ‘Flugge’ genome

by Chen, Y., Cong, L., Gong, Y., Liu, H., Ma, L., Miao, F., Song, H., Sun, J., Wang, A., Wang, Q., Wang, Z., Yan, Z., Yang, G., Yin, X.
Published 2022

GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs

by Bonnici, V., Garrison, E., Giugno, R., Pinello, L., Tognon, M.
Published 2021

qc3C: Reference-free quality control for Hi-C sequencing data

by Darling, A.E, DeMaere, M.Z
Published 2021

Efficient iterative Hi-C scaffolder based on N-best neighbors

by Durbin, R., Guan, D., McCarthy, S.A, Ning, Z., Wang, G., Wang, Y.
Published 2021

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

by Derzelle, A., Flot, J.-F, Guiglielmoni, N., Houtain, A., Van Doninck, K.
Published 2021

RESCRIPt: Reproducible sequence taxonomy reference database management

by Bokulich, N.A, Dillon, M.R, Foster, J.T, Kaehler, B.D, O'Rourke, D.R, Robeson, M.S., II, Ziemski, M.
Published 2021

2-kupl: mapping-free variant detection from DNA-seq data of matched samples

by Du, Y., Gautheret, D., Pourcel, C., Wang, Y., Xue, H.
Published 2021

LongStitch: high-quality genome assembly correction and scaffolding using long reads

by Birol, I., Coombe, L., Li, J.X, Lo, T., Nikolic, V., Warren, R.L, Wong, J.
Published 2021

SAUTE: sequence assembly using target enrichment

by Agarwala, R., Souvorov, A.
Published 2021

SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

by Chen, F., Deng, L., Fan, G., Gu, S., Guo, L., Liu, X., Seim, I., Wang, O., Wang, W., Xu, M., Xu, X., Zhao, X.
Published 2021

WEScover: selection between clinical whole exome sequencing and gene panel testing

by Alvarez, W.J, Hernandez-Ferrer, C., Kong, S.W, Lee, I.-H, Lin, Y., Mandl, K.D
Published 2021

Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation

by Cao, S., Cui, Z., Guo, H., Jiang, T., Liu, S., Liu, Y., Wang, Y.
Published 2021

SamQL: a structured query language and filtering tool for the SAM/BAM file format

by Lee, C.T, Maragkakis, M.
Published 2021

trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios

by Miller, D.B, Piccolo, S.R
Published 2021

recoup: flexible and versatile signal visualization from next generation sequencing

by Moulos, P.
Published 2021

HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

by Farrer, R.A
Published 2021

Improving structural variant clustering to reduce the negative effect of the breakpoint uncertainty problem

by Geryk, J., Korabecna, M., Simková, H., Stenzl, V., Zedníková, I., Zinkova, A.
Published 2021

Extracting multi-way chromatin contacts from Hi-C data

by Hyeon, C., Liu, L., Zhang, B.
Published 2021

Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations

by Deng, L., Farhang, A., Hoh, B.-P, Hoque, M.Z, Jong, B., Kumar, S.V, Liu, C., Lou, H., Lu, D., Marshall, C.R, Ong, R.T.-H, Phipps, M.E, Scherer, S.W, Teo, Y.-Y, Thiruvahindrapuram, B., Thuhairah, A.R, Wong, L.-P, Xie, B., Xu, S., Xu, W., Yew, C.-W, Zhang, X.
Published 2019

EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality

by Lee, K.H, MacDonald, M.L
Published 2021