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https://github.com/kdm9/seqhax

Small sequence analysis tools that don't deserve their own repos.
https://github.com/kdm9/seqhax

Last synced: 19 days ago
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Small sequence analysis tools that don't deserve their own repos.

Host: GitHub
URL: https://github.com/kdm9/seqhax
Owner: kdm9
License: gpl-3.0
Created: 2014-09-04T09:40:17.000Z (about 10 years ago)
Default Branch: master
Last Pushed: 2024-04-23T08:39:59.000Z (7 months ago)
Last Synced: 2024-10-11T19:22:59.476Z (about 1 month ago)
Language: C
Size: 2.31 MB
Stars: 8
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

Seqhax
======

A seqtk-style toolkit for sequence analysis. By no means feature complete. In
fact largely contains features other authors have not implemented in their
respective tools.

Installation
============

Seqhax is packaged in bioconda, please `mamba install -c bioconda seqhax` if conda is working for you. Otherwise, static binaries are uploaded by the CI to github releases. Or, you can build it yourself:

```bash
sudo apt-get install zlib1g-dev libhts-dev libhtscodecs-dev # Or whatever equivalent for your system
git clone https://github.com/kdmurray91/seqhax.git
cd seqhax
mkdir build && cd build
cmake ..
make
make install
```

To make static binaries, one can use `cmake -DSTATIC_BUILD=On ..` in the above series of commands.

Any other issues, file a [bug report on github](https://github.com/kdmurray91/seqhax/issues).

Documentation
=============

There are two commands in this package: `seqhax` and `htshax`.

## `seqhax`

The `seqhax` command contains various sequence file manipulation subcommands. The commands, along with a synopsis
of their actions, are displayed when one types `seqhax` with no arguments.
At the time of writing, these were:

```
$ seqhax
USAGE:
seqhax PROGRAM [options]

where PROGRAM is one of:
anon -- Rename sequences by a sequential number
convert -- Convert between FASTA and FASTQ formats
clihist -- Records a histogram of stdin.
filter -- Filter reads from a sequence file
pairs -- (De)interleave paired end reads
pecheck -- Check that paired end reads match properly
preapp -- Prepend or append string to sequences
randseq -- Generate a random sequence file
rebarcode -- Add index sequences from header to the start of reads
stats -- Basic statistics about sequence files
trunc -- Truncate sequences
```

The usage of each subcommand can be obtained using the `-h` flag to that
subcommand, e.g. `seqhax preapp -h`.

Some brief description of the more involved commands is below.

#### `pairs`

Interleaves or de-interleaves paired reads. Converts between the following
forms:

- Separate R1/R2 paired files and single read read file.
- "Strict" interleaved file, where failed/missing reads are replaced with a
single 'N'.
- "Broken paired" interleaved files, where failed/missing reads are simply not
present.

#### `pecheck`

Checks that read pairs are correctly matched, between split (R1 & R2) files, or
interleaved files. Optionally, can be used to join multiple R1/R2 from the
sample sample into a single interleaved file, while checking read IDs match.

## `htshax`

`htshax` consists of various utilities for the handling of HTS formats via HTSlib. These are mostly things that I wish samtools/bcftools would do, but don't.

```
$ htshax
Usage
htshax PROGRAM [options]

where PROGRAM is one of:

bcfhist -- Calculate histograms on MAF allele freq and missingness across samples
```

#### `bcfhist`

Create histograms over various V/BCF metrics used in variant filtering (`QUAL`, `ALLELE_FREQ`, `F_MISSING`, `INFO/DP`). Nominally bcftools stats could do this, but it doesn't summarise missingness, so I wrote this quick tool to do so.

# License

GPL v3 (see ./LICENSE).