abyss
brew install abyssGenome sequence assembler for short reads
https://www.bcgsc.ca/resources/software/abyss
License: GPL-3.0-only AND LGPL-2.1-or-later AND MIT AND BSD-3-Clause
Development: Pull requests
Formula JSON API: /api/formula/abyss.json
Formula code: abyss.rb on GitHub
Bottle (binary package) installation support provided for:
| macOS on Apple Silicon |
tahoe | ✅ |
|---|---|---|
| sequoia | ✅ | |
| sonoma | ✅ | |
| macOS on Intel |
sonoma | ✅ |
| Linux | ARM64 | ✅ |
| x86_64 | ✅ |
Current versions:
| stable | ✅ | 2.3.10 |
| head | ⚡️ | HEAD |
Revision: 1
Depends on:
| btllib | 1.7.8 | Bioinformatics Technology Lab common code library |
| open-mpi | 5.0.10 | High performance message passing library |
| libomp | 23.1.1 | LLVM's OpenMP runtime library |
Depends on when building from source:
| boost | 1.92.0 | Collection of portable C++ source libraries |
| google-sparsehash | 2.0.4 | Extremely memory-efficient hash_map implementation |
Uses from macOS: sqlite
Binaries:
ABYSS,
ABYSS-P,
AdjList,
Consensus,
DAssembler,
DistanceEst,
DistanceEst-ssq,
KAligner,
MergeContigs,
MergePaths,
Overlap,
ParseAligns,
PathConsensus,
PathOverlap,
PopBubbles,
SimpleGraph,
abyss-align,
abyss-bloom,
abyss-bloom-dbg,
abyss-bloom-dist.mk,
abyss-bowtie,
abyss-bowtie2,
abyss-bwa,
abyss-bwamem,
abyss-bwasw,
abyss-db-csv,
abyss-db-txt,
abyss-dida,
abyss-fac,
abyss-fatoagp,
abyss-filtergraph,
abyss-fixmate,
abyss-fixmate-ssq,
abyss-gapfill,
abyss-gc,
abyss-index,
abyss-junction,
abyss-kaligner,
abyss-layout,
abyss-longseqdist,
abyss-map,
abyss-map-ssq,
abyss-mergepairs,
abyss-overlap,
abyss-paired-dbg,
abyss-paired-dbg-mpi,
abyss-pe,
abyss-rresolver-short,
abyss-samtoafg,
abyss-scaffold,
abyss-sealer,
abyss-stack-size,
abyss-tabtomd,
abyss-todot,
abyss-tofastq,
konnector,
logcounter
Analytics:
| 30 days | 90 days | 365 days | |
|---|---|---|---|
| Installs | 9 | 75 | 321 |
| Installs on Request | 9 | 75 | 315 |
| Build Errors | 0 |