This is the release of Metagenome Standard Draft "Rifle Groundwater A1, ASSEMBLY_DATE=2018-03-21T16:09:06". IMG assembly of Rifle Groundwater A1, ASSEMBLY_DATE=2018-03-21T16:09:06 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165725/214645 Sequencing Project ID(s): 1006501 Input Data: Library: GXCA Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/63/17/6317.1.42246.CGTACG.fastq.gz Read Pre-processing: The number of raw input reads is: 67238846 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2901 0.2098 0.2100 0.2901 0.0000 0.0000 0.0000 0.4198 0.0880 Main genome scaffold total: 348687 Main genome contig total: 348687 Main genome scaffold sequence total: 396342069 Main genome contig sequence total: 396342069 0.000% gap Main genome scaffold N/L50: 28122/2151 Main genome contig N/L50: 28122/2151 Main genome scaffold N/L90: 226793/394 Main genome contig N/L90: 226793/394 Max scaffold length: 630552 Max contig length: 630552 Number of scaffolds > 50 KB: 357 % main genome in scaffolds > 50 KB: 9.05% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 348687 348687 396342069 396342069 100.00% 100 348687 348687 396342069 396342069 100.00% 250 348440 348440 396298962 396298962 100.00% 500 175652 175652 334233522 334233522 100.00% 1000 75093 75093 264386329 264386329 100.00% 2500 23188 23188 186777932 186777932 100.00% 5000 9641 9641 140359462 140359462 100.00% 10000 3799 3799 100285527 100285527 100.00% 25000 1040 1040 59365320 59365320 100.00% 50000 357 357 35859167 35859167 100.00% 100000 113 113 19746443 19746443 100.00% 250000 15 15 5088644 5088644 100.00% 500000 2 2 1214262 1214262 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 67238846 The number of aligned reads is: 53039473 (79%) 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