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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell.
Last modified June 28, 2016
Description: Decontaminates multiplexed assemblies via normalization and mapping.
Usage: decontaminate.sh reads=<file,file> ref=<file,file> out=<directory>
or
decontaminate.sh readnamefile=<file> refnamefile=<file> out=<directory>
Input Parameters:
reads=<file,file> Input reads, one file per library.
ref=<file,file> Input assemblies, one file per library.
readnamefile=<file> List of input reads, one line per library.
refnamefile=<file> List of input assemblies, one line per library.
interleaved=auto True forces paired/interleaved input; false forces single-ended mapping.
If not specified, interleaved status will be autodetected from read names.
unpigz=t Spawn a pigz (parallel gzip) process for faster decompression. Requires pigz to be installed.
touppercase=t (tuc) Convert lowercase letters in reads to upper case (otherwise they will not match the reference).
Output Parameters:
pigz=f Spawn a pigz (parallel gzip) process for faster compression. Requires pigz to be installed.
tmpdir=. Write temp files here. By default is uses the system's $TMPDIR or current directory.
outdir=. Write ouput files here.
Mapping Parameters:
kfilter=55 Set to a positive number N to require minimum N contiguous matches for a mapped read.
ambig=random Determines how coverage will be calculated for ambiguously-mapped reads.
first: Add coverage only at first genomic mapping location.
random: Add coverage at a random best-scoring location.
all: Add coverage at all best-scoring locations.
toss: Discard ambiguously-mapped reads without adding coverage.
Filtering Parameters:
minc=3.5 Min average coverage to retain scaffold.
minp=20 Min percent coverage to retain scaffold.
minr=18 Min mapped reads to retain scaffold.
minl=500 Min length to retain scaffold.
ratio=1.2 Contigs will not be removed by minc unless the coverage changed by at least this factor. 0 disables this filter.
mapraw=t Set true to map the unnormalized reads. Required to filter by 'ratio'.
basesundermin=-1 If positive, removes contigs with at least this many bases in low-coverage windows.
window=500 Sliding window size
windowcov=5 Average coverage below this will be classified as low.
Tadpole Parameters:
ecct=f Error-correct with Tadpole before normalization.
kt=42 Kmer length for Tadpole.
aggressive=f Do aggressive error correction.
conservative=f Do conservative error correction.
tadpoleprefilter=1 (tadpre) Ignore kmers under this depth to save memory.
Normalization Parameters:
mindepth=2 Min depth of reads to keep.
target=20 Target normalization depth.
hashes=4 Number of hashes in Bloom filter.
passes=1 Normalization passes.
minprob=0.5 Min probability of correctness to add a kmer.
dp=0.75 (depthpercentile) Percentile to use for depth proxy (0.5 means median).
prefilter=t Prefilter, for large datasets.
filterbits=32 (fbits) Bits per cell in primary filter.
prefilterbits=2 (pbits) Bits per cell in prefilter.
k=31 Kmer length for normalization. Longer is more precise but less sensitive.
Other parameters:
opfn=0 (onlyprocessfirstn) Set to a positive number to only process that many datasets. This is for internal testing of specificity.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 megs.
The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an
out-of-memory exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
JNI="-Djava.library.path=""$DIR""jni/"
JNI=""
z="-Xmx1g"
z2="-Xms1g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 15000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
decontaminate() {
local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.DecontaminateByNormalization $@"
echo $CMD >&2
eval $CMD
}
decontaminate "$@"
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