This is the release of Metagenome Standard Draft "Rifle Groundwater B1, ASSEMBLY_DATE=2018-03-21T16:13:43". IMG assembly of Rifle Groundwater B1, ASSEMBLY_DATE=2018-03-21T16:13:43 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1166034/215263 Sequencing Project ID(s): 1006507 Input Data: Library: HSBH Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/63/18/6318.5.42196.GGTAGC.fastq.gz Read Pre-processing: The number of raw input reads is: 118243274 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2820 0.2181 0.2175 0.2823 0.0000 0.0000 0.0000 0.4356 0.1039 Main genome scaffold total: 471838 Main genome contig total: 471838 Main genome scaffold sequence total: 548729601 Main genome contig sequence total: 548729601 0.000% gap Main genome scaffold N/L50: 38364/2222 Main genome contig N/L50: 38364/2222 Main genome scaffold N/L90: 304764/404 Main genome contig N/L90: 304764/404 Max scaffold length: 754755 Max contig length: 754755 Number of scaffolds > 50 KB: 512 % main genome in scaffolds > 50 KB: 9.14% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 471838 471838 548729601 548729601 100.00% 100 471838 471838 548729601 548729601 100.00% 250 471274 471274 548624244 548624244 100.00% 500 244040 244040 466719724 466719724 100.00% 1000 105315 105315 370366595 370366595 100.00% 2500 33068 33068 261897486 261897486 100.00% 5000 13179 13179 193689408 193689408 100.00% 10000 5203 5203 139205293 139205293 100.00% 25000 1470 1470 83404586 83404586 100.00% 50000 512 512 50174652 50174652 100.00% 100000 133 133 24868226 24868226 100.00% 250000 22 22 8680444 8680444 100.00% 500000 5 5 3119339 3119339 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 118243274 The number of aligned reads is: 99153295 (84%) 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