This is the release of Metagenome Standard Draft "Rifle Groundwater D1, ASSEMBLY_DATE=2018-03-21T16:09:52". IMG assembly of Rifle Groundwater D1, ASSEMBLY_DATE=2018-03-21T16:09:52 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1166244/215683 Sequencing Project ID(s): 1006519 Input Data: Library: CZBG Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/61/81/6181.5.39405.fastq.gz Read Pre-processing: The number of raw input reads is: 287488874 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.3027 0.1974 0.1972 0.3027 0.0000 0.0000 0.0000 0.3945 0.1207 Main genome scaffold total: 151329 Main genome contig total: 151329 Main genome scaffold sequence total: 187721266 Main genome contig sequence total: 187721266 0.000% gap Main genome scaffold N/L50: 8016/3430 Main genome contig N/L50: 8016/3430 Main genome scaffold N/L90: 91471/367 Main genome contig N/L90: 91471/367 Max scaffold length: 485912 Max contig length: 485912 Number of scaffolds > 50 KB: 248 % main genome in scaffolds > 50 KB: 12.27% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 151329 151329 187721266 187721266 100.00% 100 151329 151329 187721266 187721266 100.00% 250 150096 150096 187488814 187488814 100.00% 500 61794 61794 156685307 156685307 100.00% 1000 32058 32058 135273452 135273452 100.00% 2500 11609 11609 104332570 104332570 100.00% 5000 5145 5145 82055653 82055653 100.00% 10000 2257 2257 62032403 62032403 100.00% 25000 677 677 37903846 37903846 100.00% 50000 248 248 23027423 23027423 100.00% 100000 62 62 10593807 10593807 100.00% 250000 9 9 3079190 3079190 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 287488874 The number of aligned reads is: 253543697 (88%) 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