This is the release of Metagenome Standard Draft "Rifle Groundwater C2, ASSEMBLY_DATE=2018-03-21T16:16:45". IMG assembly of Rifle Groundwater C2, ASSEMBLY_DATE=2018-03-21T16:16:45 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165727/214649 Sequencing Project ID(s): 1006516 Input Data: Library: CZBN Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/61/81/6181.7.39407.fastq.gz Read Pre-processing: The number of raw input reads is: 271669124 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2573 0.2427 0.2428 0.2573 0.0000 0.0000 0.0000 0.4855 0.1126 Main genome scaffold total: 916984 Main genome contig total: 916984 Main genome scaffold sequence total: 1062611143 Main genome contig sequence total: 1062611143 0.000% gap Main genome scaffold N/L50: 76824/2196 Main genome contig N/L50: 76824/2196 Main genome scaffold N/L90: 580701/382 Main genome contig N/L90: 580701/382 Max scaffold length: 923412 Max contig length: 923412 Number of scaffolds > 50 KB: 990 % main genome in scaffolds > 50 KB: 9.49% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 916984 916984 1062611143 1062611143 100.00% 100 916984 916984 1062611143 1062611143 100.00% 250 915408 915408 1062327191 1062327191 100.00% 500 472265 472265 909076811 909076811 100.00% 1000 213697 213697 726771359 726771359 100.00% 2500 64569 64569 502651953 502651953 100.00% 5000 25193 25193 368223920 368223920 100.00% 10000 9666 9666 262216447 262216447 100.00% 25000 2637 2637 157235267 157235267 100.00% 50000 990 990 100858755 100858755 100.00% 100000 298 298 53449376 53449376 100.00% 250000 48 48 17776411 17776411 100.00% 500000 7 7 4251258 4251258 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 271669124 The number of aligned reads is: 231063616 (85%) 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