Elementolab/SNVseeqer Pipeline Tutorial

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  • paired-end, RefSeq
$SNVSEEQERDIR/SCRIPTS/PBS_quickAlignPE.pl --fastq1=s_1_1_sequence.txt.gz --fastq2=s_1_2_sequence.txt.gz --submit=1 --numcpus=4
$SNVSEEQERDIR/SCRIPTS/PBS_SNPseeqerPB_RefSeq --files="*.sam" --detectreadlen=1  --submit=1
  • single-end, RefSeq
$SNVSEEQERDIR/SCRIPTS/PBS_quickAlign.pl --fastq=s_8_sequence.txt.gz --submit=1 --numcpus=4
$SNVSEEQERDIR/SCRIPTS/PBS_SNPseeqerPB_RefSeq --files="*.gz" --detectreadlen=1  --submit=1
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