Uparse/Qime pipeline
module add vsearch/1.11.1
module add mothur/1.37.3
module load usearch/9.0.2132

>python fastq_strip_barcode_relabel2.py SAMR1.fastq NNNNNNNNNNNNNNNNNNNNNN barcode_16.fasta Seq 
>usearch -fastq_eestats SAMR1.strip.fastq -output SAMR1_eestats.txt
>usearch -fastq_filter SAMR1_2016.strip.fastq -fastq_maxee 1 -fastq_minlen 250 -fastaout SAMR1_2016.strip.trim.fasta
>usearch -fastq_filter Sam_R1_2014.strip.fastq -fastq_maxee 1 -fastq_minlen 250 -fastaout Sam_R1_2014.strip.trim.fasta
>usearch -fastx_truncate  culture.fa -trunclen 250 -fastaout culture.trim.fa
>usearch -derep_fulllength SAMR1_2016.strip.trim.fasta -fastaout SAMR1_2016.strip.trim.unique.fasta -sizeout
>usearch -derep_fulllength Sam_R1_2014.strip.trim.fasta -fastaout SamR1_2014.strip.trim.unique.fasta -sizeout
>usearch -derep_fulllength culture.trim.fa -fastaout culture.trim.unique.fa -sizeout
>usearch -sortbysize SAMR1_2016.strip.trim.unique.fasta -fastaout SAMR1_2016.strip.trim.sorted.unique.fasta -minsize 1
>usearch -sortbysize SamR1_2014.strip.trim.unique.fasta -fastaout SamR1_2014.strip.trim.unique.sorted.fasta -minsize 1
>usearch -sortbysize culture.trim.unique.fa -fastaout culture.trim.unique.sorted.fasta -minsize 1
>cat  culture.trim.unique.sorted.fasta SamR1_2014.strip.trim.unique.sorted.fasta SAMR1_2016.strip.trim.sorted.unique.fasta > 14_16_ITScc.fasta
>usearch -sortbysize 14_16_ITScc.fasta -fastaout 14_16_ITScc.sorted.fasta 
>usearch -cluster_otus 14_16_ITScc.sorted.fasta -otu_radius_pct 3 -otus 14_16_ITScc.sorted.otu.97.fasta -relabel OTU_ -sizein -sizeout
>usearch -uchime_ref 14_16_ITScc.sorted.otu.97.fasta -db /srv/scratch/z3219366/Uparse_fungal/unite_its1.fa -uchimeout results.uchime -strand plus
>usearch -usearch_global  14_16_ITScc.sorted.fasta  -db 14_16_ITScc.sorted.otu.97.fasta -strand plus -id 0.97 -uc 14_6_ITScc.97.readmap.uc
>python /srv/scratch/z3219366/Uparse_fungal/uc2otutab.py 14_6_ITScc.97.readmap.uc > 14_16_ITScc.97.otu_table.txt
>usearch -utax 14_16_ITScc.sorted.otu.97.fasta -db /srv/scratch/z3219366/Uparse_fungal/unite_its1.fa -taxconfs /srv/scratch/z3219366/Uparse_fungal/its1.tc -tt /srv/scratch/z3219366/Uparse_fungal/unite.tt -> utaxout 14_16_ITScc.97.otu.taxonomy.txt
>usearch -usearch_global  14_16_ITScc.sorted.fasta  -db 14_16_ITScc.sorted.otu.97.fasta -strand plus -id 0.97 -mothur_shared_out mothur.otutable.txt
>usearch -usearch_global 14_16_ITScc.sorted.fasta -db 14_16_ITScc.sorted.otu.97.fasta -strand plus -id 0.97 -biomout otu_table.biom


mothur > make.shared(biom=otu_table.biom)
#Delete all cultured samples, and the SIM samples so we only have _14_16 ITS seqsuences
mothur > rarefaction.single(shared=otu_table.shared, calc=sobs, freq=100)
#We want to count the number of samples in each group and sub-sample to at least 1000 sequences
mothur > count.seqs(shared=otu_table.shared)
mohur> count.groups(count=otu_table.userLabel.count_table)
mothur > sub.sample(shared=otu_table.shared, size=1066)
mothur > rarefaction.single(shared=otu_table.userLabel.subsample.shared)