Sign Tools 4 Torrent
Sign Tools 4 Torrent
Sign Tools 4 Torrent
for medical applications, the ngs analytical pipeline starts with the step of base calling, where the physical signals (either images or electrical signals) are translated to sequences of nucleotide bases. the output of this step is a sequence file composed of a set of reads in the fastq format as in illumina technology or in the unaligned bam format as in ion torrent technology. (the read is the sequence of a dna fragment). the bam file is the binary version of the readable sam text file [ 14 ]. the fastq/sam/bam format includes the ngs reads and related quality scores [ 14 ]. the next step of the pipeline is to align the ngs reads to the reference human genome. the output of this step is a file in the sam/bam format with alignment information. ion torrent machines have a built in software for base calling and alignment, called torrent suite ( ). the torrent suite delivers the sequencing results in unaligned bam format. if the user runs the alignment and variant calling workflow, then the reads are aligned to the reference human genome and the results are kept in an aligned bam format. the unaligned reads are kept as well in the aligned bam file but without mapping information. the unaligned bam file is deleted after the successful generation of the bam file.
in step 4.4, we tested different sequence clustering options in terms of number of otus and their taxonomic assignment. we first ran the clustering algorithm on the its sequences for each sample as a starting point for the tuning of the clustering parameters. from these results, we selected the clustering options that achieved the highest number of otus with the lowest number of chimeras. the following clustering options were applied: uclust ( ), qiime ( ), and usearch ( ).
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