This is the release of Metagenome Standard Draft "Rifle Groundwater B2, ASSEMBLY_DATE=2018-03-21T16:12:01". IMG assembly of Rifle Groundwater B2, ASSEMBLY_DATE=2018-03-21T16:12:01 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165832/214859 Sequencing Project ID(s): 1006510 Input Data: Library: CZBB Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/63/18/6318.3.42194.GTTTCG.fastq.gz Read Pre-processing: The number of raw input reads is: 90503350 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2414 0.2587 0.2584 0.2415 0.0000 0.0000 0.0000 0.5171 0.1129 Main genome scaffold total: 319261 Main genome contig total: 319261 Main genome scaffold sequence total: 360293882 Main genome contig sequence total: 360293882 0.000% gap Main genome scaffold N/L50: 20997/2444 Main genome contig N/L50: 20997/2444 Main genome scaffold N/L90: 204862/365 Main genome contig N/L90: 204862/365 Max scaffold length: 727880 Max contig length: 727880 Number of scaffolds > 50 KB: 448 % main genome in scaffolds > 50 KB: 12.36% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 319261 319261 360293882 360293882 100.00% 100 319261 319261 360293882 360293882 100.00% 250 318856 318856 360226798 360226798 100.00% 500 131956 131956 293796955 293796955 100.00% 1000 65486 65486 246381962 246381962 100.00% 2500 20402 20402 178682936 178682936 100.00% 5000 8337 8337 137151212 137151212 100.00% 10000 3417 3417 103341722 103341722 100.00% 25000 1156 1156 69037693 69037693 100.00% 50000 448 448 44535236 44535236 100.00% 100000 129 129 22754233 22754233 100.00% 250000 17 17 5917274 5917274 100.00% 500000 2 2 1452403 1452403 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 90503350 The number of aligned reads is: 73858296 (82%) Assembly Methods: The assembly was produced by the JGI IMG team as part of their effort to reassemble older projects with modern assembly tools. The steps are similar to the current JGI Assembly protocol (as of 7/2017) with the notable exception of the treatment of contaminants. The JGI Assembly group filters for quality and contaminants prior to assembly, however this assembly was produced by the IMG group using the raw/unfiltered reads and contaminant contigs are treated differently. Large eukaryote contaminant contigs (human, mouse, cat, dog) are discarded but suspected prokaryote contigs are not removed and are listed in the contaminants.txt file instead. Users should be aware that microbes indicated in the contaminants file are commonly found in sequencing libraries, being introduced from the reagents used in library preparation. The raw/unfiltered reads were read corrected using bfc (r181) with kmer size of 21. The resulting reads were then assembled using SPAdes assembler (SPAdes version: 3.10.0-dev) (3) using a range of Kmers with the following options: --meta --only-assembler -k 21,33,55,77,99,127 The entire filtered read set was mapped to the final assembly and coverage information generated using bwa mem (4; version 0.7.15-r1142-dirty) using default parameters. Contaminant contigs were identified by mapping to the JGI Assembly group's standard human, dog, cat, and mouse reference databases; contigs with >= 90% length match were discarded. Putative contaminant contigs were identified by mapping contigs to JGI Assembly group's standard microbial contaminants reference database and contigs with >= 90% length match are listed in the contaminants.txt file, but not removed. If you have any questions, please contact the JGI project manager. Please indicate if your questions pertain to the IMG reassembly or the official JGI assembly. (1) B. Bushnell: BBTools software package (http://bbtools.jgi.doe.gov) (2) Li, H. BFC: correcting Illumina sequencing errors. Bioinformatics 31, 2885-2887 (2015). Doi: 10.1093/bioinformatics/btv290 (https://github.com/lh3/bfc) (3) Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834. (4) Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168] The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231