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<code> #! /bin/bash -x # # Example assembly of 100bp C. elegans data set. The only argument # this script takes is the overlap length used for the final contig assembly. # # We assume the data is downloaded from the SRA and converted to fastq files # Set IN1 and IN2 to be the paths to the data on your filesystem IN1=SRR065390_1.fastq IN2=SRR065390_2.fastq # Parameters SGA_BIN=sga-0.9.31 # Overlap parameter used for the final assembly. This is the only argument # to the script OL=75 # The number of threads to use CPU=8 # To save memory, we index $D reads at a time then merge the indices together D=4000000 # Correction k-mer value CK=41 # The minimum k-mer coverage for the filter step. Each 27-mer # in the reads must be seen at least this many times COV_FILTER=2 # Overlap parameter used for FM-merge. This value must be no greater than the minimum # overlap value you wish to try for the assembly step. MOL=55 # Parameter for the small repeat resolution algorithm R=10 # The number of pairs required to link two contigs into a scaffold MIN_PAIRS=5 # The minimum length of contigs to include in a scaffold MIN_LENGTH=200 # Distance estimate tolerance when resolving scaffold sequences SCAFFOLD_TOLERANCE=1 # Turn off collapsing bubbles around indels MAX_GAP_DIFF=0 # First, preprocess the data to remove ambiguous basecalls $SGA_BIN preprocess --pe-mode 1 -o SRR065390.fastq $IN1 $IN2 # # Error correction # # Build the index that will be used for error correction # As the error corrector does not require the reverse BWT, suppress # construction of the reversed index $SGA_BIN index -a ropebwt -t $CPU --no-reverse SRR065390.fastq # Perform error correction with a 41-mer. # The k-mer cutoff parameter is learned automatically $SGA_BIN correct -k $CK --discard --learn -t $CPU -o reads.ec.k$CK.fastq SRR065390.fastq # # Contig assembly # # Index the corrected data. $SGA_BIN index -a ropebwt -t $CPU reads.ec.k$CK.fastq # Remove exact-match duplicates and reads with low-frequency k-mers $SGA_BIN filter -x $COV_FILTER -t $CPU --homopolymer-check --low-complexity-check reads.ec.k$CK.fastq # Merge simple, unbranched chains of vertices $SGA_BIN fm-merge -m $MOL -t $CPU -o merged.k$CK.fa reads.ec.k$CK.filter.pass.fa # Build an index of the merged sequences $SGA_BIN index -d 1000000 -t $CPU merged.k$CK.fa # Remove any substrings that were generated from the merge process $SGA_BIN rmdup -t $CPU merged.k$CK.fa # Compute the structure of the string graph $SGA_BIN overlap -m $MOL -t $CPU merged.k$CK.rmdup.fa # Perform the contig assembly without bubble popping # Scaffolding/Paired end resolution # CTGS=assemble.m$OL-contigs.fa GRAPH=assemble.m$OL-graph.asqg.gz # Realign reads to the contigs ~/work/devel/sga/src/bin/sga-align --name celegans.pe $CTGS $IN1 $IN2 # Make contig-contig distance estimates ~/work/devel/sga/src/bin/sga-bam2de.pl -n $MIN_PAIRS --prefix libPE celegans.pe.bam # Make contig copy number estimates ~/work/devel/sga/src/bin/sga-astat.py -m $MIN_LENGTH celegans.pe.refsort.bam > libPE.astat $SGA_BIN scaffold -m $MIN_LENGTH --pe libPE.de -a libPE.astat -o scaffolds.n$MIN_PAIRS.scaf $CTGS $SGA_BIN scaffold2fasta -m $MIN_LENGTH -a $GRAPH -o scaffolds.n$MIN_PAIRS.fa -d $SCAFFOLD_TOLERANCE --use-overlap --write-unplaced scaffolds.n$MIN_PAIRS.scaf </code>