---
name: "bowtie"
section: "1"
platform: "linux"
package: "bowtie"
version: "1.3.1-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bowtie"
---

# bowtie(1)

ultrafast memory-efficient short read aligner

## NAME

bowtie-align-s - ultrafast memory-efficient short read aligner

## DESCRIPTION

usage: bowtie \[-h\] \[--verbose\] \[--debug\] \[--large-index\]

### options:

- **-h**, **--help**

  show this help message and exit

**--verbose**

**--debug**

**--large-index**

64-bit Built on Debian-reproducible Thu, 25 Jan 2024 12:27:31 +0100 Compiler: gcc version 13.2.0 Options: **-O3** **-Wl**,--hash-style=both **-DPOPCNT\_CAPABILITY** **-Wdate-time** **-D\_FORTIFY\_SOURCE**=*2* **-g** **-O2** **-ffile-prefix-map=**.=. **-fstack-protector-strong** **-fstack-clash-protection** **-Wformat** **-Werror**=*format-security* **-fcf-protection**  **-g** **-O2** **-ffile-prefix-map=**.=. **-fstack-protector-strong** **-fstack-clash-protection** **-Wformat** **-Werror**=*format-security* **-fcf-protection** **-std**=*c*++03 **-Wl**,-z,relro **-Wl**,-z,now Sizeof {int, long, long long, void\*, size\_t, off\_t}: {4, 8, 8, 8, 8, 8}