obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Complete release notes and change obiannotate options accordingly

Browse Source 
Former-commit-id: 947db1f4606d57893cf758df57a4c954e3949e6b
This commit is contained in:
Eric Coissac
2023-05-02 11:01:26 +02:00
parent 60c187404d
commit bffcab1096
2 changed files with 15 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
Release-notes.md
View File

@ -31,6 +31,20 @@
obidistribute --pattern "pcr_reads/sample_%s_R1.fastq" -c sample tagged_library_R1.fastq
obidistribute --pattern "pcr_reads/sample_%s_R2.fastq" -c sample tagged_library_R2.fastq
```
- Adding of two options **--add-lca-in** and **--lca-error** to `obiannotate`. These options aim to help during
construction of reference database using `obipcr`. On obipcr output, it is commonly run obiuniq. To merge
identical sequences annotated with different taxids, it is now possible to use the following strategie :
```{bash}
obiuniq -m taxid myrefdb.obipcr.fasta \
| obiannotate -t taxdump --lca-error 0.05 --add-lca-in taxid \
> myrefdb.obipcr.unique.fasta
```
The `obiuniq` call merge identical sequences keeping track of the diversity of the taxonomic annotations in the
`merged_taxid` slot, while `obiannotate` loads a NCBI taxdump and computes the lowest common ancestor of the taxids represented in `merged_taxid`. By specifying **--lca-error** 0.05, we indicate that we allow for at most 5% of the taxids disagreeing with the computed LCA. The computed LCA is stored in the slot specified as a parameter of the option **--add-lca-in**. Scientific name and actual error rate corresponding to the estimated LCA are also stored in the sequence annotation.
### Enhancement
- Rename the `forward_mismatches` and `reverse_mismatches` from instanced by `obimutiplex` into