This is the release of Metagenome Standard Draft "Rifle Groundwater F1, ASSEMBLY_DATE=2018-03-21T16:11:06". IMG assembly of Rifle Groundwater F1, ASSEMBLY_DATE=2018-03-21T16:11:06 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165932/215059 Sequencing Project ID(s): 1006531 Input Data: Library: GXCB Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/63/17/6317.1.42246.GAGTGG.fastq.gz Read Pre-processing: The number of raw input reads is: 65137348 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2825 0.2178 0.2176 0.2821 0.0000 0.0000 0.0000 0.4354 0.1152 Main genome scaffold total: 177394 Main genome contig total: 177394 Main genome scaffold sequence total: 229674359 Main genome contig sequence total: 229674359 0.000% gap Main genome scaffold N/L50: 9991/3036 Main genome contig N/L50: 9991/3036 Main genome scaffold N/L90: 108594/419 Main genome contig N/L90: 108594/419 Max scaffold length: 825227 Max contig length: 825227 Number of scaffolds > 50 KB: 316 % main genome in scaffolds > 50 KB: 14.09% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 177394 177394 229674359 229674359 100.00% 100 177394 177394 229674359 229674359 100.00% 250 177090 177090 229619245 229619245 100.00% 500 90209 90209 198383562 198383562 100.00% 1000 39922 39922 163495313 163495313 100.00% 2500 12758 12758 122439677 122439677 100.00% 5000 5411 5411 97305055 97305055 100.00% 10000 2483 2483 77340062 77340062 100.00% 25000 891 891 53055508 53055508 100.00% 50000 316 316 32367421 32367421 100.00% 100000 94 94 17306180 17306180 100.00% 250000 15 15 5777176 5777176 100.00% 500000 1 1 825227 825227 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 65137348 The number of aligned reads is: 56222068 (86%) 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