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Manage sequence alignments

Project description

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

Project details


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