This is the release of Metagenome Standard Draft "Rifle Groundwater E1, ASSEMBLY_DATE=2018-03-21T16:02:07". IMG assembly of Rifle Groundwater E1, ASSEMBLY_DATE=2018-03-21T16:02:07 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165833/214861 Sequencing Project ID(s): 1006525 Input Data: Library: GOAU Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/63/17/6317.1.42246.ATCACG.fastq.gz Read Pre-processing: The number of raw input reads is: 76504828 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2878 0.2120 0.2129 0.2873 0.0000 0.0000 0.0000 0.4249 0.1339 Main genome scaffold total: 116899 Main genome contig total: 116899 Main genome scaffold sequence total: 179869898 Main genome contig sequence total: 179869898 0.000% gap Main genome scaffold N/L50: 4700/5188 Main genome contig N/L50: 4700/5188 Main genome scaffold N/L90: 61830/421 Main genome contig N/L90: 61830/421 Max scaffold length: 875117 Max contig length: 875117 Number of scaffolds > 50 KB: 306 % main genome in scaffolds > 50 KB: 18.33% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 116899 116899 179869898 179869898 100.00% 100 116899 116899 179869898 179869898 100.00% 250 116451 116451 179788001 179788001 100.00% 500 55915 55915 159203222 159203222 100.00% 1000 29357 29357 140160499 140160499 100.00% 2500 11032 11032 112068370 112068370 100.00% 5000 4909 4909 91001480 91001480 100.00% 10000 2211 2211 72560353 72560353 100.00% 25000 823 823 51406468 51406468 100.00% 50000 306 306 32961325 32961325 100.00% 100000 105 105 19639111 19639111 100.00% 250000 16 16 6328351 6328351 100.00% 500000 3 3 2283043 2283043 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 76504828 The number of aligned reads is: 66634175 (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