This is the release of Metagenome Standard Draft "Rifle Groundwater D2, ASSEMBLY_DATE=2018-03-21T16:08:12". IMG assembly of Rifle Groundwater D2, ASSEMBLY_DATE=2018-03-21T16:08:12 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165515/214225 Sequencing Project ID(s): 1006522 Input Data: Library: CZBP Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/63/18/6318.3.42194.TTAGGC.fastq.gz Read Pre-processing: The number of raw input reads is: 86270490 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2810 0.2190 0.2190 0.2810 0.0000 0.0000 0.0000 0.4380 0.1141 Main genome scaffold total: 188436 Main genome contig total: 188436 Main genome scaffold sequence total: 252834057 Main genome contig sequence total: 252834057 0.000% gap Main genome scaffold N/L50: 11638/3133 Main genome contig N/L50: 11638/3133 Main genome scaffold N/L90: 110257/444 Main genome contig N/L90: 110257/444 Max scaffold length: 513242 Max contig length: 513242 Number of scaffolds > 50 KB: 342 % main genome in scaffolds > 50 KB: 15.19% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 188436 188436 252834057 252834057 100.00% 100 188436 188436 252834057 252834057 100.00% 250 187919 187919 252736929 252736929 100.00% 500 100032 100032 222743605 222743605 100.00% 1000 47175 47175 185214295 185214295 100.00% 2500 15547 15547 137340063 137340063 100.00% 5000 6366 6366 105745859 105745859 100.00% 10000 2485 2485 79077965 79077965 100.00% 25000 769 769 53455921 53455921 100.00% 50000 342 342 38415977 38415977 100.00% 100000 126 126 23457842 23457842 100.00% 250000 29 29 9719850 9719850 100.00% 500000 1 1 513242 513242 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 86270490 The number of aligned reads is: 74689166 (87%) 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