Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: edlib

https://packages.ecosyste.ms/registries/pypi.org/packages/edlib

Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
18 versions
Latest release: over 3 years ago
18 dependent packages
45,448 downloads last month

Papers Mentioning edlib 11

Alignment and mapping methodology influence transcript abundance estimation
Cited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: over 4 years ago

10.7717/peerj.4925

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
Cited by: 166
Author(s): Jonathan M. Palmer, Michelle A. Jusino, Mark T. Banik, Daniel L. Lindner
Software Mentions: 8
Published: over 6 years ago

10.1186/s13059-021-02474-0

Gramtools enables multiscale variation analysis with genome graphs
Cited by: 13
Author(s): Brice Letcher, Martin Hunt, Zamin Iqbal
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02483-z

Trycycler: consensus long-read assemblies for bacterial genomes
Cited by: 128
Author(s): Ryan R. Wick, Louise M. Judd, Louise Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-018-2014-8

Introducing difference recurrence relations for faster semi-global alignment of long sequences
Cited by: 69
Author(s): Hajime Suzuki, Masahiro Kasahara
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12915-021-01141-x

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone
Cited by: 56
Author(s): Amrita Srivathsan, Leshon Lee, Kazutaka Katoh, Emily Hartop, Sujatha Narayanan Kutty, Johnathan Wong, Darren C. J. Yeo, Rudolf Meier
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-020-02090-4

Producing polished prokaryotic pangenomes with the Panaroo pipeline
Cited by: 327
Author(s): Gerry Tonkin‐Hill, Neil MacAlasdair, Christopher Ruis, Aaron Weimann, Gal Horesh, John A. Lees, Rebecca A. Gladstone, Stephanie Lo, Christopher Beaudoin, R. Andres Floto, Simon D. W. Frost, Jukka Corander, Stephen D. Bentley, Julian Parkhill
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-020-01974-9

Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing
Cited by: 5
Author(s): Alexander Dilthey, Sebastian Meyer, Achim J. Kaasch
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13059-020-02244-4

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
Cited by: 24
Author(s): Guillaume Holley, Doruk Beyter, Helga Ingimundardóttir, Peter L. Møller, Snædís Kristmundsdóttir, Hannes P. Eggertsson, Bjarni V. Halldórsson
Software Mentions: 1
Published: almost 4 years ago

10.1093/bioinformatics/btaa1034

SVIM-asm: structural variant detection from haploid and diploid genome assemblies
Cited by: 35
Author(s): David Heller, Martin Vingron
Software Mentions: 1
Published: about 4 years ago

10.3390/s20247244

Simulation of Nanopore Sequencing Signals Based on BiGRU
Cited by: 7
Author(s): Weigang Chen, Peng Zhang, Lifu Song, Jinsheng Yang, Changcai Han
Software Mentions: 1
Published: about 4 years ago