{% extends "template.html" %} {% block table_of_contents %}
Figure 1.1: Ridge plot showing the length distribution of input reads.
{% endblock %} {% block read_len_table %}Table 1.1: Uniform read length for each sample.
Sample | Length |
---|---|
{{ row.Sample }} | {{ row.Length }} |
Prior to subsequent analysis, reads are filtered for length and ambiguous sequence content.
Any read comprised of more than {{"{:.0f}".format(ambiguous_read_threshold * 100)}}% ambiguous bases (N
) is discarded.
Reads less than {{"{:,}".format(read_length_threshold)}} bp in length are also excluded from all subsequent analysis.
(These thresholds can be configured with the --ambiguous-thresh
and --length-thresh
arguments.)
Table 1.2: Read filtering metrics.
Sample | Total Reads | Filtered (Ambiguous) | Filtered (Length) | Reads Kept |
---|---|---|---|---|
{{sample}} | {{stats.total_reads}} | {{stats.filtered_ambig}} | {{stats.filtered_length}} | {{stats.retention}} |
Filtered reads are aligned to marker reference sequences using BWA MEM and formatted, sorted, and indexed using SAMtools.
{% endblock %}