forked from biobakery/MetaPhlAn
-
Notifications
You must be signed in to change notification settings - Fork 0
/
changeset.txt
executable file
·23 lines (20 loc) · 1.32 KB
/
changeset.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
=== Version 3.0
* New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
* Estimation of metagenome composed by unknown microbes with parameter `--unknown_estimation`
* Automatic retrieval and installation of the latest MetaPhlAn database with parameter `--index latest`
* Virus profiling with `--add_viruses`
* Calculation of metagenome size for improved estimation of reads mapped to a given clade
* Inclusion of NCBI taxonomy ID in the ouput file
* CAMI (Taxonomic) Profiling Output Format included
* Removal of reads with low MAPQ values
=== Version 2.2.0
- added option "marker_counts" (by Nicola)
=== Version 2.1.0
- added min_alignment_len option to filter out short alignments in local mode. For long reads (>150) it is now recommended to use local mapping together with "--min_alignment_len 100" to filter out very short alignments. (by Tin)
- added "--samout" option to store the mapping file in SAM format (the SAM will be compressed if the extension of the specified output file ends with ".bz2") (by Tin)
- fix: MetaPhlAn2 now ingores about ~300 markers that were a-specific (thanks to Eric)
=== Version 2.0.0
- fix: Biom >= 2.0.0 has the clade IDs second and the sample ids third'
- added extract_markers.py
- fix: #5; revamp biom generation; set clade IDs as enumeration
- added utils/metaphlan2krona.py