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Manage sequence alignments

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Manage sequence alignments


pip3 install seqalign


pip3 install --user seqalign


with SequenceAlignment(<path to input BAM or FASTQ file>) as sa:
    sa.cleans_up_bam = False
    sa.write(<path to output BAM file>)


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.

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