Published November 6, 2019
| Version v.1.0
Dataset
Open
MACREL software benchmark data set: Simulated metagenomes with sequencing quality, errors profile and abundance distributions derived from real samples
- 1. Fudan University
Description
These metagenomes were used in the benchmarking of FACS pipeline, and were designed after NGLess benchmark dataset (doi.org/10.5281/zenodo.2560288). Metagenomes were simulated with ART-bin-MountRainier-2016.06.05 using real abundance profiles (.abund files) available elsewhere, and proGenomes' representative contigs as reference genomes. There are available metagenomes with 40, 60 and 80 M (million of reads) based in the reference genomes and abundances of the following samples:
SAMEA2466916
SAMEA2466953
SAMEA2466965
SAMEA2621107
SAMEA2621229
SAMEA2621247
To convert them from the CRAM format back to fastq files:
## 1. converting from cram to bam format:
samtools view -b -T refgenome.fa -o file.bam file.cram
## 2. sorting the bam file:
samtools sort -n file.bam -o input_sorted.bam # sort reads by identifier-name (-n)
## 3. converting from bam to fastq format:
bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
Files
Files
(47.0 GB)
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md5:366fe8cc20b48ea555f97b7a7039676d
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1.8 GB | Download |
md5:b17828703b51cc8366c8259a3fac7a46
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1.7 GB | Download |
md5:fd1041dd9dc6805697aa365e699ec304
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1.7 GB | Download |
md5:5691a41fb6ea92c956cfec917744c94b
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1.7 GB | Download |
md5:d0a49282dc1de838527fc070fd0373df
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1.7 GB | Download |
md5:58e47f8865d36af069e771b7200befe3
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1.7 GB | Download |
md5:268a5c6afd961d59287dfc3fec3a0107
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2.6 GB | Download |
md5:f078e0659cb88ffd2c8ac8b12f60c08b
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2.6 GB | Download |
md5:ea23bb3bf54e615034de42c39ce9cbc4
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2.6 GB | Download |
md5:ade80da0f512f6bbf2d3063dc04ecd6e
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2.6 GB | Download |
md5:abdc3cd139a190dca1a7067e8a5b6adf
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2.6 GB | Download |
md5:61b7a50b92b6eb15ea6f144b9e78ade0
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2.6 GB | Download |
md5:462689bede06d059c1fe41eb38add115
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3.5 GB | Download |
md5:b873f4c0571327092ea0fa211c54abe4
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3.5 GB | Download |
md5:f960d8bc3151cd1f0554f82df3f59a48
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3.5 GB | Download |
md5:4f9336a4110581644169de0198c42b4f
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3.5 GB | Download |
md5:a48a549984800d75612592c5f785e292
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3.5 GB | Download |
md5:4dd5f79b38be04f5f2b9a22355aa2c76
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3.4 GB | Download |
Additional details
References
- Alves, Renato, Coelho, Luis Pedro, Huerta-Cepas, Jaime, & Bork, Peer. (2019). Simulated metagenomes with quality and abundance distributions derived from real samples (Version 1.0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.2560288