Patrick D. Schloss, PhD (@PatSchloss)
Department of Microbiology & Immunology
http://bit.ly/EDAMAME_mothur_2018
AltMetrics:
# Samples | #F Primers | #R Primers | Reads/Sample* |
---|---|---|---|
96 | 12 | 8 | 156250 |
192 | 12 | 16 | 78125 |
384 | 24 | 16 | 39062 |
1536 | 48 | 32 | 9766 |
Region | Length | Error rate after making contigs (%) | Error rate after pre.cluster (%) |
---|---|---|---|
V3-V4 | 429 | 0.41 | 0.26 |
V4 | 253 | 0.04 | 0.01 |
V4-V5 | 375 | 0.57 | 0.26 |
"V3-V5" | 260 | 0.06 | 0.02 |
Sample | V3-V4 | V4 | V4-V5 |
---|---|---|---|
Mock - PC(20) | NA | 21.4 | 83.5 |
Mock - actual | NA | 32.4 | 126.2 |
Mouse | NA | 135.7 | 145.7 |
Human | NA | 121.6 | 187.8 |
Soil | NA | 1271.3 | 1221.2 |
Region | Length | 250PE error rate after making contigs (%) | 300PE error rate after pre.cluster (%) |
---|---|---|---|
V3-V4 | 429 | 0.41 | 0.80 |
V4 | 253 | 0.04 | 0.04 |
V4-V5 | 375 | 0.57 | 0.90 |
"V3-V5" | 260 | 0.06 | NA |
method | what it does... | reference |
---|---|---|
make.contigs |
assemble reads | Kozich et al. 2014 |
screen.seqs |
remove bad reads | |
unique.seqs |
collapse duplicate reads | |
count.seqs |
count frequency of each sequence in each sample | |
align.seqs |
align sequences to a reference | Schloss 2009, Schloss 2010 |
filter.seqs |
trim reads to same alignment space | Schloss 2013 |
pre.cluster |
remove one and two offs | Schloss et al. 2011 |
chimera.uchime |
identify and remove chimeras | Edgar et al. 2011 |
classify.seqs |
classify sequences against a database | Wang et al. 2009 |
remove.lineage |
remove contaminants | |
cluster.split |
assign sequences to OTUs | Schloss & Westcott 2011 |
phylotype |
assign sequences to phylotypes | |
make.shared |
generate sample by OTU frequency table | |
clearcut |
generate a neighbor-joining tree | Sheneman et al. 2006 |
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mothur-1.39.5
AMI