Binning reads Files

You can find here all script files and supplementary materials of the paper entitled "Binning de Sequencias Anterior à Montagem em Metagenomas: um estudo de caso", available at http://...

Files were organized into 7 folders, as follows:

| docs: Folder which contains supplementary docs with additional information
| subsampling: Folder which contains the scripts used to produce subsample files for downstream analysis
 ---| subsampling_low.sh: Script to generate low complexity subsample
 ---| subsampling_medium.sh: Script to generate medium complexity subsample
 ---| subsampling_high.sh: Script to generate high complexity subsample
| diversity_coverage: Folder which contains the scripts used to estimate the level of coverage in each metagenomic dataset
 ---| nonpareil_sub_low.sh: Script to generate the estimate of diversity of low complexity subsample
 ---| nonpareil_sub_medium.sh: Script to generate the estimate of diversity of medium complexity subsample
 ---| nonpareil_sub_high.sh: Script to generate the estimate of diversity of high complexity subsample
----| nonpareil_low.sh: Script to generate the estimate of diversity of low complexity original sample
 ---| nonpareil_medium.sh: Script to generate the estimate of diversity of medium complexity original sample
 ---| nonpareil_high.sh: Script to generate the estimate of diversity of high complexity original sample
| taxonomic_binning: Folder with scripts to perform taxonomic binning (based on Kaiju classification)
 ---| kaiju.sh: Script to generate Kaiju classifications for each sample
 ---| kaiju_binner: binning tool developed to cluster reads by taxonomy
     ---| src: Python source codes
         ---| group_read_ids_by_taxon: Program to group read ids by their taxonomy
         ---| separate_reads_by_ids: Program to collect read information of read groups and produce FASTQ files 
     ---| script.sh: Script to process Kaiju output files and then produce taxonomic bins of reads
     ---| read_ids.tar.gz: Read ids used for taxonomic binning
| genomic_binning: Folder with scripts to perform genomic binning
     ---| metaprob.sh: Script perform genomic binning using MetaProb
     ---| fa2fq.py: Script to produce FASTQ files for each bin from MetaProb
| assemblies: Folder with scripts to assemble reads into contigs
 ---| taxonomic_bins: Scripts and assembly results of taxonomic bins
     ---| megahit.sh: Script for assembling each taxonomic bin (output contigs are available in file assemblies.tar.gz)
     ---| assemblies.tar.gz: Final assemblies for taxonomic binning
 ---| genomic_bins: Scripts and assembly results of genomic bins
     ---| assemblies.tar.gz: Final assemblies for genomic binning
     ---| genomic_bins: Taxonomic description of each bin and merged clusters
     ---| megahit.sh: Script for assembling each genomic bin (output contigs are available in file assemblies.tar.gz)
 ---| no_binning: Scripts and assembly results of assembly with no binning
     ---| assemblies.tar.gz: Final assemblies without binning
     ---| megahit.sh: Script for assembling each sample (output contigs are available in file assemblies.tar.gz)
| evaluation: Scripts to evaluate assemblies
 ---| checkm.sh: Script for assessing diversity coverage of taxonomic and genomic approaches
 ---| metaquast.sh: Script for assessing assemblies quality of both taxonomic and genomic approaches
 ---| fragGene.sh: Script to analyze CDS for each assembly
 ---| fragGeneCounter.R: R Script to be executed on each output of FragGene (listed on fragGene.sh)
 ---| taxonomic_list: List of reference taxons used for MetaQuast evaluation of taxonomic binning
 ---| genomic_list: List of reference taxons used for MetaQuast evaluation of genomic binning
 ---| no_binning_list: List of reference taxons used for MetaQuast evaluation of assembly with no binning