Man pages for pgpmartin/NanoBAC
Analysis of long read (Oxford Nanopore, PacBio) data from BAC or large plasmid sequencing
| AnnotateBACreads | Annotate BAC reads |
| blaST2GR | Convert an imported blast result table to a GRanges |
| checkBlastVar | Check if an object was imported using 'readBlast' or import... |
| consensusFromMSF | Obtain the consensus sequence from an MSF file |
| consmat2seq | Get the consensus sequence from a consensus matrix |
| estimateBACsizeFromVDV | Estimate the size of a BAC using the length of all VDV reads |
| FilterBACreads | Select specific reads from a table of BAC read annotations... |
| findVDVjunctions | Find the vector-insert junctions at the beginning and end of... |
| getDVDnames | Identify DVD reads based on alignment of the vector on the... |
| getVDnames | Identify VD reads based on alignment of the vector on the... |
| getVDVnames | Identify VDV reads based on alignment of the vector on the... |
| makeVarseq | Introduce variations in a DNA sequence |
| paf2gr | Convert an paf file imported with 'read_paf' to a 'GRanges' |
| readBlast | Read a blast result file (currently only for files created... |
| read_paf | Read a .paf file such as produced by minimap/minimap2. |
| SelectSingularBlastALN | Filter a blast result table for alignment overlapping other... |
| selectVDVreads | Select VDV reads from a set of Nanopore reads |
| splitDVDreads | Select DVD reads from a set of Nanopore reads and split the... |
| TestArg | Test if the argument of a function is of a given class or... |
| tidy_paf_tags | Tidy the flag columns imported from a paf file |
