49 research outputs found
SILVA 138.1 SSURef NR99 database formatted for phyloFlash
No full textSmall-subunit ribosomal RNA reference database from SILVA release 138.1, formatted for use with phyloFlash (https://github.com/HRGV/phyloFlash) (version >=3.4). phyloFlash is a pipeline for rapid screening and targeted assembly of SSU rRNA sequences from short-read metagenomic or transcriptomic datasets.
Please see README.md for more details and license information
SILVA 138.1 SSURef NR99 (main taxonomic ranks only) formatted for phyloFlash
No full text<p>Small-subunit ribosomal RNA reference database from SILVA release 138.1, (taxonomy with main ranks only) formatted for use with phyloFlash (https://github.com/HRGV/phyloFlash) (version >=3.4). phyloFlash is a pipeline for rapid screening and targeted assembly of SSU rRNA sequences from short-read metagenomic or transcriptomic datasets.</p><p>Please see README.md for more details and license information.</p>
HRGV/phyloFlash: phyloFlash v3.3 beta 1
No full text<p>release for archiving with zenodo</p>
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
No full textMotivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license
Supplementary data (comparison of multiple metagenomes) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
No full textUsage example for phyloFlash, comparison of multiple metagenomes by SSU rRNA taxonomic profile.
The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b
cokelaer/fitter: v1.2.3 synchronised on pypi
No full textuse logging module instead of prints
add fitter standalone application
add progress ba
Supplementary data (low-diversity metagenome and reference database completeness) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
No full textComparison of phyloFlash and Matam on low-diversity platyhelminth metagenome, showing effect of reference database completeness on results.
The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b
Analysis of 23S rRNA genes in metagenomes – A case study from the Global Ocean Sampling Expedition
No full text
