ATLAS - Three commands to start analyzing your metagenome data
Assembly/fasta/{sample}.fasta
reads: QC/reads/{sample}_{fraction}.fastq.gz
Seemless update: If you update atlas and continue on an old project. Your old files will be copies. Or the path defined in the sample.tsv will be used.
https://github.com/metagenome-atlas/atlas/pull/683
In this new version, Atlas uses binning with co-abundance as default. While binning each sample individually is faster, using co-abundance for binning, by quantifying the coverage of contigs across multiple samples provides valuable insights about contig co-variation.
Starting with version 2.18, atlas places every sample in a single BinGroup and defaults to vamb as the binner unless there are very few samples. For fewer than 8 samples, metabat is the default binner.
The defaults are fine except when you have many samples (>150) where atlas gives a warning that you should put sour samples in more than one bin group.
Previously each sample was put in its own BinGroup optimized for single-sample binning. Running vamb in those versions would consider all samples, regardless of their BinGroup. Hence updating to v2.18 might cause errors if using a sample.tsv file from an older Atlas version. You can resolve this by assigning a unique BinGroup to each sample.
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.17.2...v2.18.0
The tool Skani claims to be better and faster than the combination of mash + FastANI as used by dRep
I implemented the skin for species clustering.
We now do the species clustering in the atlas run binning
step.
So you get information about the number of dereplicated species in the binning report. This allows you to run different binners before choosing the one to use for the genome annotation.
Also, the file storage was improved all important files are in Binning/{binner}/
My custom species clustering does the following steps:
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.16.3...v2.17.0
Save GTDB v8 in download folder for GTDB v8 Thanky to @strejcem
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.15.2...v2.16.1
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.15.1...v2.15.2
Binning
Thank you @trickovicmatija for your help.
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.13.1...v2.14.0
genome_filter_criteria: "(Completeness-5*Contamination >50 ) & (Length_scaffolds >=50000) & (Ambigious_bases <1e6) & (N50 > 5*1e3) & (N_scaffolds < 1e3)"
The genome filtering is similar as other publications in the field, e.g. GTDB. What is maybe a bit different is that genomes with completeness around 50% and contamination around 10% are excluded where as using the default parameters dRep would include those.
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.12.0...v2.13.0