seqalign 0.1.2

Manage sequence alignments

seqalign

Manage sequence alignments

Installation

pip3 install seqalign

or

pip3 install --user seqalign

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.