---
name: "sand_align_kernel"
section: "1"
platform: "linux"
package: "coop-computing-tools"
version: "1:7.14.5-1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sand_align_kernel"
---

# sand\_align\_kernel(1)

align candidate sequences sequentially

## NAME

**sand\_align\_kernel** - align candidate sequences sequentially

## SYNOPSIS

FCsand\_align\_kernel \[options\] \[input file\]FT

## DESCRIPTION

**sand\_align\_kernel** aligns candidate sequences sequentially. It is not normally called by the user, but is invoked by **[sand\_align\_master(1)](/sand_align_master/1.md)** for each sequential step of a distributed alignment workload.  The options to **sand\_align\_kernel** control the type of alignment (Smith-Waterman, Prefix-Suffix, Banded, etc) and the quality threshhold for reporting alignments.  These options are typically passed in by giving the **-e** option to **sand\_align\_master**.

**sand\_align\_kernel** reads a list of sequences from the given input file, or from standard input if none is given. The sequences are in the compressed fasta format produced by **[sand\_compress\_reads(1)](/sand_compress_reads/1.md)**.  The first sequence in the input is compared against all following sequences until a separator line. Following the separator, the next sequence is compared against all following sequences until the following separator, and so on.

## OPTIONS

- **-a *\<sw\|ps\|banded\>***

  Specify the type of alignment: sw (Smith-Waterman), ps (Prefix-Suffix), or banded.  If not specified, default is banded.

- **-o *\<ovl\|ovl\_new\|align\|matrix\>***

  Specify how each alignment should be output: ovl (Celera V5, V6 OVL format), ovl\_new (Celera V7 overlap format), align (display the sequences and alignment graphically) or matrix (display the dynamic programming matrix).  **[sand\_align\_master(1)](/sand_align_master/1.md)** expects the ovl output format, which is the default.  The other formats are useful for debugging.

- **-m *\<length\>***

  Minimum aligment length (default: 0).

- **-q *\<quality\>***

  Minimum match quality (default: 1.00)

- **-x**

  Delete input file after completion.

- **-d *\<subsystem\>***

  Enable debugging for this subsystem.  (Try **-d all** to start.

- **-v**

  Show program version.

- **-h**

  Display this message.

## EXIT STATUS

On success, returns zero.  On failure, returns non-zero.

## EXAMPLES

Users do not normally invoke sand\_align\_kernel directly.  Instead, pass arguments by using the **-e** option to **[sand\_align\_master(1)](/sand_align_master/1.md)**.  For example, to specify a minimum alignment length of 5 and a minimum quality of 0.25:

```

```

-

  % sand\_align\_master sand\_align\_kernel -e "-m 5 -q 0.25" mydata.cand mydata.cfa mydata.ovl

## COPYRIGHT

The Cooperative Computing Tools are Copyright (C) 2022 The University of Notre Dame.  This software is distributed under the GNU General Public License.  See the file COPYING for details.

## SEE ALSO

- •

  **Cooperative Computing Tools Documentation**

- •

  **SAND User Manual**

- •

  **[sand\_filter\_master(1)](/sand_filter_master/1.md)**  **[sand\_filter\_kernel(1)](/sand_filter_kernel/1.md)**  **[sand\_align\_master(1)](/sand_align_master/1.md)**  **[sand\_align\_kernel(1)](/sand_align_kernel/1.md)**  **[sand\_compress\_reads(1)](/sand_compress_reads/1.md)**  **[sand\_uncompress\_reads(1)](/sand_uncompress_reads/1.md)**  **[work\_queue\_worker(1)](/work_queue_worker/1.md)**