- Getting a lightning-specific error with hisat2
Each aligner runs in its own environment, which is in the envs directory.
Install them all as follows:
cd envs
ls | xargs -I {} conda env create -f {}
At the time of testing, all of the aligners have the same version number in both macOS-arm64 and linux-64 except bbmap.
| Program | macOS-arm64 | linux-64 | Notes |
|---|---|---|---|
| bbmap | 39.77 | 39.79 | |
| blast-legacy | 2.2.26 | 2.2.26 | |
| bowtie2 | 2.5.5 | 2.5.5 | |
| bwa | 0.7.19 | 0.7.19 | |
| gmap | 2025.07.31 | 2025.07.31 | broken |
| hisat2 | 2.2.2 | 2.2.2 | |
| minimap2 | 2.30 | 2.30 | |
| pblat | 2.5.1 | 2.5.1 | semi-broken on MacOS |
| segemehl | 0.3.4 | 0.3.4 | |
| star | 2.7.11b | 2.7.11b | broken on MacOS |
| subread | 2.1.1 | 2.1.1 |
Sequence sources
| Name | File | Notes |
|---|---|---|
| random | random.fa.gz |
created with randomseq.py |
| genome | at1pct.fa.gz |
from init/data |
| mRNA | at1pct-mRNA.fa.gz |
from extract-transcripts.py |
Read sources
- Randomly generated reads decorated with 0-20% error
- Mock reads created by
badread(not done yet)