Manage sequence alignments
Project description
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.
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