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Items: 1 to 20 of 109

1.

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH.

Bioinformatics. 2019 Nov 15. pii: btz848. doi: 10.1093/bioinformatics/btz848. [Epub ahead of print]

PMID:
31730192
2.

Struo: a pipeline for building custom databases for common metagenome profilers.

de la Cuesta-Zuluaga J, Ley RE, Youngblut ND.

Bioinformatics. 2019 Nov 28. pii: btz899. doi: 10.1093/bioinformatics/btz899. [Epub ahead of print]

PMID:
31778148
3.

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment.

Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O'Flynn C.

PLoS One. 2019 Jun 10;14(6):e0214354. doi: 10.1371/journal.pone.0214354. eCollection 2019.

4.

swga: a primer design toolkit for selective whole genome amplification.

Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D.

Bioinformatics. 2017 Jul 15;33(14):2071-2077. doi: 10.1093/bioinformatics/btx118.

5.

MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).

Stewart RD, Auffret MD, Snelling TJ, Roehe R, Watson M.

Bioinformatics. 2019 Jun 1;35(12):2150-2152. doi: 10.1093/bioinformatics/bty905.

6.

MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes.

Ward LM, Shih PM, Fischer WW.

Bioinformatics. 2018 Dec 15;34(24):4284-4286. doi: 10.1093/bioinformatics/bty510.

PMID:
29939199
7.

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates.

Ecale Zhou CL, Malfatti S, Kimbrel J, Philipson C, McNair K, Hamilton T, Edwards R, Souza B.

Bioinformatics. 2019 Nov 1;35(21):4402-4404. doi: 10.1093/bioinformatics/btz258.

8.

ISDB: a database toolkit for storing and analyzing viral integration site data.

Sibley TR, Silberman EJ, Mullins JI.

Bioinformatics. 2019 Mar 15;35(6):1073-1075. doi: 10.1093/bioinformatics/bty712.

PMID:
30165425
9.

LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.

Hanson NW, Konwar KM, Hallam SJ.

Bioinformatics. 2016 Dec 1;32(23):3535-3542. Epub 2016 Aug 11.

10.

CharGer: clinical Characterization of Germline variants.

Scott AD, Huang KL, Weerasinghe A, Mashl RJ, Gao Q, Martins Rodrigues F, Wyczalkowski MA, Ding L.

Bioinformatics. 2019 Mar 1;35(5):865-867. doi: 10.1093/bioinformatics/bty649.

PMID:
30102335
11.

NextPolish: a fast and efficient genome polishing tool for long read assembly.

Hu J, Fan J, Sun Z, Liu S.

Bioinformatics. 2019 Nov 28. pii: btz891. doi: 10.1093/bioinformatics/btz891. [Epub ahead of print]

PMID:
31778144
12.

SnapperDB: a database solution for routine sequencing analysis of bacterial isolates.

Dallman T, Ashton P, Schafer U, Jironkin A, Painset A, Shaaban S, Hartman H, Myers R, Underwood A, Jenkins C, Grant K.

Bioinformatics. 2018 Sep 1;34(17):3028-3029. doi: 10.1093/bioinformatics/bty212.

PMID:
29659710
13.

Knot_pull-python package for biopolymer smoothing and knot detection.

Jarmolinska AI, Gambin A, Sulkowska JI.

Bioinformatics. 2019 Aug 16. pii: btz644. doi: 10.1093/bioinformatics/btz644. [Epub ahead of print]

PMID:
31504154
14.

FORESEE: a tool for the systematic comparison of translational drug response modeling pipelines.

Turnhoff LK, Hadizadeh Esfahani A, Montazeri M, Kusch N, Schuppert A.

Bioinformatics. 2019 Oct 1;35(19):3846-3848. doi: 10.1093/bioinformatics/btz145.

15.

svtools: population-scale analysis of structural variation.

Larson DE, Abel HJ, Chiang C, Badve A, Das I, Eldred JM, Layer RM, Hall IM.

Bioinformatics. 2019 Nov 1;35(22):4782-4787. doi: 10.1093/bioinformatics/btz492.

16.

geck: trio-based comparative benchmarking of variant calls.

Kómár P, Kural D.

Bioinformatics. 2018 Oct 15;34(20):3488-3495. doi: 10.1093/bioinformatics/bty415.

17.

miComplete: weighted quality evaluation of assembled microbial genomes.

Hugoson E, Lam WT, Guy L.

Bioinformatics. 2019 Aug 22. pii: btz664. doi: 10.1093/bioinformatics/btz664. [Epub ahead of print]

PMID:
31504158
18.

ISEScan: automated identification of insertion sequence elements in prokaryotic genomes.

Xie Z, Tang H.

Bioinformatics. 2017 Nov 1;33(21):3340-3347. doi: 10.1093/bioinformatics/btx433.

PMID:
29077810
19.

SGTK: a toolkit for visualization and assessment of scaffold graphs.

Kunyavskaya O, Prjibelski AD.

Bioinformatics. 2019 Jul 1;35(13):2303-2305. doi: 10.1093/bioinformatics/bty956.

PMID:
30475983
20.

PyRanges: efficient comparison of genomic intervals in Python.

Stovner EB, Sætrom P.

Bioinformatics. 2019 Aug 2. pii: btz615. doi: 10.1093/bioinformatics/btz615. [Epub ahead of print]

PMID:
31373614

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