---
name: "sambamba"
section: "1"
platform: "linux"
package: "sambamba"
version: "1.0.1+dfsg-2+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sambamba"
---

# sambamba(1)

toolkit for working with SAM/BAM files

## NAME

**sambamba** - toolkit for working with SAM/BAM files

## SYNOPSIS

**sambamba** \[subcommand\] \[arguments...\]

## DESCRIPTION

**sambamba** unifies several independent tools in one executable:

- •

  [sambamba-view(1)](/sambamba-view/1.md)

- •

  [sambamba-index(1)](/sambamba-index/1.md)

- •

  [sambamba-merge(1)](/sambamba-merge/1.md)

- •

  [sambamba-sort(1)](/sambamba-sort/1.md)

- •

  [sambamba-markdup(1)](/sambamba-markdup/1.md)

- •

  [sambamba-flagstat(1)](/sambamba-flagstat/1.md)

- •

  [sambamba-slice(1)](/sambamba-slice/1.md)

- •

  [sambamba-pileup(1)](/sambamba-pileup/1.md)

-

  Thus available subcommands are *view*, *index*, *merge*, *sort*, *markdup*, *flagstat*, *slice*, and *mpileup*. Their use is explained on the corresponding man pages.

Note that sambamba uses all available cores by default.