seqalign
Manage sequence alignments
Installation
pip install seqalign
or
pip install --user seqalign
If you have not already installed picardtools, you will also need to run:
picardtools-download
Examples
with SequenceAlignment(<path to input BAM or FASTQ file>) as sa:
sa.cleans_up_bam = False
sa.remove_supplementary_alignments()
sa.samtools_sort(memory_limit=10)
sa.samtools_index()
sa.write(<path to output BAM file>)
Notes
The input_file
argument to SequenceAlignment()
should be a string for
single-end reads or for data that is already aligned. For raw paired-end reads,
it should be a tuple containing two strings giving the paths to the two
FASTA / FASTQ files.
Command line usage
seqalign
includes a couple of pre-built pipelines for aligning ChIP-seq and ATAC-seq data.
They rely on certain environment variables being set, as described here
To see the basic command line documentation, simply enter seqalign
at the terminal:
seqalign
There are two commands for aligning sequencing data:
`seqalign-chip-seq` and `seqalign-atac-seq`. See their
respective documentation by running:
seqalign-chip-seq --help
seqalign-atac-seq --help