Man pages for alexpiper/seqateurs
Tools for trimming and processing sequence data
| align_overlap | Minimum overlap between a query and reference |
| bbdemux | Demultiplex fusion primers using BBmap Seal |
| bbdemux2 | Demultiplex fusion primers using BBmap Seal |
| bbmap_install | Install BBtools |
| bbsplit | Split interleaved reads |
| bbsplit2 | Split interleaved reads |
| bbtrim | Trim primers using BBDuk |
| bbtrim2 | Trim primers using BBDuk |
| clr | Centred log-ratio transformation |
| clrInv | Inverse clr log-ratio transformation |
| cluster_otus | OTU clustering of DADA2 seqtab |
| coalesce_join | Coalescing join |
| codon_filter | Filter sequences containing stop codons |
| create_logsheet | Create logsheet |
| create_mismatch | Create_mismatch |
| create_samplesheet | Create Samplesheet |
| dot-findExecutable | Find executable |
| estimate_trunclen | Automatically estimate trunclen for filtering |
| expit | Inverse logitt transofmration |
| fast_melt | Fast melt |
| fastqc | Run FastQC Tool |
| fastqc_install | fastqc_install |
| get_qual_stats | Get qual stats |
| get_reading_frame | Get Reading frame of sequences |
| gm_mean | Geometric mean |
| logit | Logit transformation |
| lowest_classified | Get the lowest classified ranks for the OTUs |
| na_to_unclassified | Convert NA classifications to the their highest successful... |
| n_overlap | Number of bases overlapping between forward and reverse reads |
| parse_aqhist | Parse average quality histograms from bbtrim |
| parse_bbdemux | Parse appended bbdemux logs into tidy format |
| parse_bbtrim | Parse appended bbtrim logs into tidy format |
| parse_bhist | parse base frequency histograms from bbtrim |
| parse_gchist | Parse GC content histograms from bbtrim |
| parse_lhist | Parse sequence length histograms from bbtrim |
| parse_qhist | Parse quality score histograms from bbtrim |
| parse_seqrun | Parse seqrun |
| pipe | Pipe operator |
| plot_lengths | Plot readlengths of fastq |
| plot_maxEE | MaxEE plot |
| plot_quality | Quality plot |
| propagate_tax | Propagate taxonomy |
| proportions | Convert phyloseq table to proportions #' |
| ps_to_dnabin | ps_to_dnabin |
| ps_to_fasta | output a FASTA file from a phyloseq object |
| summarise_index | Summarise index |
| summarise_taxa | Summarise_taxa |
| unclassified_to_na | Convert classifications that are annotated with their highest... |
