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yuf17006 committed Jun 29, 2018
1 parent cf45d92 commit 8fdb74ae83932ebb729fb147162902c1010412cb
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  1. +93 −0 submissionscripts/all.hits
  2. +17 −0 submissionscripts/assembly.sh
  3. +17 −0 submissionscripts/autest.sh
  4. +16 −0 submissionscripts/bbcsub.bash
  5. +69 −0 submissionscripts/contigtrimmer.pl
  6. +70 −0 submissionscripts/extein.pl
  7. +15 −0 submissionscripts/ictest.bash
  8. +15 −0 submissionscripts/iqtree.sh
  9. +16 −0 submissionscripts/kraken.sh
  10. +14 −0 submissionscripts/metabat.pl
  11. +14 −0 submissionscripts/metabat.sh
  12. +18 −0 submissionscripts/metagenomepipeline/0assembly.sh
  13. +16 −0 submissionscripts/metagenomepipeline/1trim.sh
  14. +16 −0 submissionscripts/metagenomepipeline/2map.sh
  15. +16 −0 submissionscripts/metagenomepipeline/3samtobam.bash
  16. +16 −0 submissionscripts/metagenomepipeline/4samsort.bash
  17. +14 −0 submissionscripts/metagenomepipeline/5genomecov.bash
  18. +280 −0 submissionscripts/metagenomepipeline/Metagenome Pipeline.ipynb
  19. +573 −0 submissionscripts/metagenomepipeline/gilist.txt
  20. +6,530 −0 submissionscripts/metagenomepipeline/intein.db
  21. BIN submissionscripts/metagenomepipeline/intein.db.phr
  22. BIN submissionscripts/metagenomepipeline/intein.db.pin
  23. BIN submissionscripts/metagenomepipeline/intein.db.psq
  24. +16 −0 submissionscripts/metagenomepipeline/inteinseq.sh
  25. +170 −0 submissionscripts/metagenomepipeline/metagenomepipeline.sh
  26. +102 −0 submissionscripts/metagenomepipeline/mg.int.sorted
  27. +88 −0 submissionscripts/metagenomepipeline/pipeline.sh
  28. +26 −0 submissionscripts/metagenomepipeline/short.tsbh
  29. +20 −0 submissionscripts/metagenomepipeline/sig.mgcds.txt
  30. +16 −0 submissionscripts/nrblast.sh
  31. +17 −0 submissionscripts/nrgiextract.sh
  32. +12 −0 submissionscripts/parse.py
  33. +16 −0 submissionscripts/prokka.sh
  34. +16 −0 submissionscripts/psiblast.sh
  35. +17 −0 submissionscripts/raxml.bash
  36. +16 −0 submissionscripts/tblastn.sh
  37. +3 −0 submissionscripts/test.fna
  38. +16 −0 submissionscripts/transeq.sh
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@@ -0,0 +1,17 @@
#!/bin/bash
#SBATCH --job-name=raxml
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 16
#SBATCH --partition=amd
#SBATCH --mail-type=END
#SBATCH --mem=20G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o racks_%j.out
#SBATCH -e racks_%j.err



module load RAxML/8.2.11
raxmlHPC ­f i ­t extein.te ­z inteinaa.align.ufboot ­m GTRCAT ­n T4

@@ -0,0 +1,17 @@
#!/bin/bash
#SBATCH --job-name=tblastn
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 6
#SBATCH --partition=amd
#SBATCH --mail-type=END
#SBATCH --mem=250G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o tblastn_%j.out
#SBATCH -e tblastn_%j.err



module load iqtree/1.5.5
iqtree-omp -s inteinaa.align -st AA -m LG+F+I+G4 -n 0 -z exteinaa.ufb -zb 1000 -au -nt AUTO
iqtree-omp -s exteinaa.align -st AA -m LG+F+R5 -n 0 -z inteinaa.ufb -zb 1000 -au -nt AUTO
@@ -0,0 +1,16 @@
#!/bin/bash
#$ -N ass
#$ -M yutian.feng@uconn.edu
#$ -q all.q
#$ -m ea
#$ -S /bin/bash
#$ -cwd
#$ -pe smp 16
#$ -o ass_$JOB_ID.out
#$ -e ass_$JOB_ID.err

cd /home/yuf17006/metagenomes
module load SPAdes/3.10.0
spades.py --meta --only-asembler --pe<1>-1 ERR1739731_1.fastq --pe<1>-2 ERR1739731_2.fastq -o test1


@@ -0,0 +1,69 @@
#!/usr/bin/perl -w

use strict;


my $infasta=$ARGV[0];

open FH1 , "$infasta" or die "$!";



my @sequence ="";
my $first = "";
my $second ="";
my $begin="";
my $end="";
my $front = "";
my $back = "";
my $final = "";
while(<FH1>){
chomp;
@sequence = split /\t/, $_;
$first = $sequence[6];
$second = $sequence[7];
if ($first > $second) {
$begin = $second;
$end = $first;
}
else{
$begin = $first;
$end = $second;
}
my $frontflank = int($begin)-1000;
my $backflank = int($end+1000);
my $seqname = $sequence[0];
open FH2, "$seqname".".seqfile";
my $worthless ="";
my $cds= "";
while(<FH2>){
chomp;
if(/^\>(.*)/){
$worthless = $worthless . $_;
}
else{
$cds = $cds . $_;
}
}

my @readin = split //, $cds;


while ($frontflank < $backflank){
$front = $front . $readin[$frontflank];
$frontflank += 1;

}

$final = $front ;

print ">".$sequence[0].".seqfile2\n".$final."\n";
@sequence ="";
$front ="";
$final ="";
$back ="";
$first = "";
$second ="";
$begin="";
$end="";
}
@@ -0,0 +1,70 @@
#!/usr/bin/perl -w

use strict;


my $infasta=$ARGV[0];

open FH1 , "$infasta" or die "$!";



my @sequence ="";
my $first = "";
my $second ="";
my $begin="";
my $end="";
my $front = "";
my $back = "";
my $final = "";
while(<FH1>){
chomp;
@sequence = split /\t/, $_;
$first = $sequence[6];
$second = $sequence[7];
if ($first > $second) {
$begin = $second;
$end = $first;
}
else{
$begin = $first;
$end = $second;
}
my $seqname = $sequence[0];
open FH2, "$seqname".".seqfile2";
my $worthless ="";
my $cds= "";
while(<FH2>){
chomp;
if(/^\>(.*)/){
$worthless = $worthless . $_;
}
else{
$cds = $cds . $_;
}
}

my @readin = split //, $cds;
my $i =0;

while ($i < $begin){
$front = $front . $readin[$i];
$i += 1;
}

while ($end < $#readin){
$back = $back . $readin[$end];
$end += 1;
}
$final = $front . $back;

print ">".$sequence[0].".ext\n".$final."\n";
@sequence ="";
$front ="";
$final ="";
$back ="";
$first = "";
$second ="";
$begin="";
$end="";
}
@@ -0,0 +1,15 @@
#!/bin/bash
#SBATCH --job-name=raxml
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 16
#SBATCH --partition=amd
#SBATCH --mail-type=END
#SBATCH --mem=20G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o racks_%j.out
#SBATCH -e racks_%j.err


module load RAxML/8.2.11
raxmlHPC -f i -t extein.te -z inteinaa.align.ufboot -m GTRCAT -n T4
@@ -0,0 +1,15 @@
#!/bin/bash
#SBATCH --job-name=reroot
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 6
#SBATCH --partition=amd
#SBATCH --mail-type=END
#SBATCH --mem=50G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o reroot_%j.out
#SBATCH -e reroot_%j.err


module load iqtree/1.5.5
iqtree-omp -s cdsall7.align -nt AUTO -bb 1000 -st AA
@@ -0,0 +1,16 @@
#!/bin/bash
#SBATCH --job-name=kraken
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 24
#SBATCH --partition=himem4
#SBATCH --mail-type=END
#SBATCH --mem=250G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o kraken_%j.out
#SBATCH -e kraken_%j.err



module load kraken/1.0
kraken -d /isg/shared/databases/kraken/standard contigs.fasta --threads 24
@@ -0,0 +1,14 @@
#!/bin/bash
#SBATCH --job-name=metabat
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 24
#SBATCH --partition=himem4
#SBATCH --mail-type=END
#SBATCH --mem=250G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o metabat_%j.out
#SBATCH -e metabat_%j.err

module load metabat/2.12.1
metabat -i contigs.fasta.gz -o binout
@@ -0,0 +1,14 @@
#!/bin/bash
#SBATCH --job-name=metabat
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 24
#SBATCH --partition=himem4
#SBATCH --mail-type=END
#SBATCH --mem=250G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o metabat_%j.out
#SBATCH -e metabat_%j.err

module load metabat/2.12.1
metabat -i contigs.fasta.gz -o binout
@@ -0,0 +1,18 @@
#!/bin/bash
#SBATCH --job-name=assing
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 16
#SBATCH --partition=himem4
#SBATCH --mail-type=END
#SBATCH --mem=500G
#SBATCH --mail-user=yutian.feng@uconn.edu
#SBATCH -o assing_%j.out
#SBATCH -e assing_%j.err



module load SPAdes/3.11.1

spades.py --pe1-1 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739732_1.trim.fq --pe1-2 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739732_2.trim.fq -o assembly2
spades.py --pe1-1 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739731_1.trim.fq --pe1-2 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739731_2.trim.fq -o assembly3

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