ArticleBMC research notes2012
BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler.
Article in BMC research notes, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
6 citing papers in PubMed.
- Potential application of a newly isolated phage BUCT609 infectingFrontiers in microbiology · 2022Article
- Cadasides, Calcium-Dependent Acidic Lipopeptides from the Soil Metagenome That Are Active against Multidrug-Resistant Bacteria.Journal of the American Chemical Society · 2019Article
- Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.Nature communications · 2018Article
- Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens.Nature microbiology · 2018Article
- VTBuilder: a tool for the assembly of multi isoform transcriptomes.BMC bioinformatics · 2014Article
- Genomic insights into tuberculosis.Nature reviews. Genetics · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAs more and more reference genome sequences are assembled, it becomes practical to assemble individual genomes from large amount of raw read data based on a reference sequence. However, most available assembly tools are designed for de-novo genome assembly. There is one commercial tool box (Newbler) developed for re-sequencing projects based on the Roche 454 sequencing platform. However, the genome with large repeat regions cannot be well assembled in Newbler.
findingsWe developed a new sequence assembly tool (BIGrat, Beijing Institute of Genomics Re-Assembly Tool) for pyrosequencing-based re-sequencing projects, such as data generated from Roche 454 and IonTorrent platforms. BIGrat improves the output of Newbler when evaluated on genome assemblies including chloroplast, mitochondrial, bacterial, and plant nuclear genomes.
conclusionWe presented a novel sequence assembly tool BIGrat for pyrosequencing-based re-sequencing projects, which can easily be integrated into Newbler pipelines for next-generation sequencing assembly and analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.