The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation... R Leinonen,H Sugawara,M Shumway - 《Nucleic Acids Resear...
We show that quality-score guided error correction can improve the assembly accuracy of several datasets from the NCBI SRA (Short-Read Archive) in terms of N50-values as well as runtime. We further propose a number of improvements of to our previously published CUDA-EC algorithm to improve ...
Single-nucleotide variants SRA: Sequence Read Archive WGS: Whole genome sequencing NCBI: National Center for Biotechnology Information References Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, et al. GAGE: a critical ev...
Raw sequencing data and thede novohybrid assembly were submitted to NCBI Sequence Read Archive (SRA)65and NCBI Genbank66under the accession number PRJNA576869. References Wernli, D.et al. Antimicrobial resistance: The complex challenge of measurement to inform policy and the public.PLOS Med.14, ...
The data that support the findings of this study are available from Sequence Read Archive (SRA). N0015, N13532 and M0253 are under accession number SRR3493407, SRX4395160 and SRX4395159, respectively. The simulated data used in this study can be generated and a detailed tutorial is openly ...
beensubmittedtoNCBIShortReadArchive(http://.ncbi.nlm.nih.gov/Traces/sra/sra.cgi)underaccessionno. SRA010040.] Genomesarethefundamentalunitbywhichaspeciescanbede- finedandformthefoundationfordecipheringhowanorganism develops,lives,dies,andisaffectedbydisease.Inaddition,com- ...
Availability of data and materials The raw sequencing data can be accessed in the Sequence Read Archive (SRA) database under the accession number PRJNA1034104.Abbreviations Abx: Antibiotic cocktail BEC: Blood ethanol concentration DEG: Differentially expressed genes DeSeq2 : Differential expression...
The parameterinspecifies the input files to read, which may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred. The assembled contigs will be stored in${name}-contigs.faand the scaffolds will be stored in${name}-scaffolds....
coverage. Each catalog is a single FASTA file containing the sequences, the header identifiers contain the Sequence Read Archive (SRA) identifiers. The catalogues can be downloadedhere. We provide aHH-suite3database called "BFD" containing sequences from the Metaclust, SRC, MERC and Uniport a...
Previously published datasets of MNase-seq with G1 yeast cells were obtained from the Sequence Read Archive (SRA) with accession number SRP04131440. The MNase-seq data were first cleaned using Trim Galore (Version 0.6.7) and mapped to the S288c reference genome (SGD, SacCer3) using bowtie...