Differences

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--- minion_sequencing_from_start_to_finish [2017/12/15 00:12] – 24.138.65.117
+++ minion_sequencing_from_start_to_finish [2021/09/06 10:43] (current) – 134.190.232.139
@@ Line 2: / Line 2: @@
 {{ :minionheart.jpg?400 |}}
-Documentation by Sarah Shah
+Documentation by Sarah Shah and Jon Jerlström Hultqvist
 This is a general protocol for monitoring and dealing with a MinION sequencing run.
@@ Line 45: / Line 45: @@
 The "read_fast5_basecaller.py" line should be repeated for each input folder. Add the ** - - barcoding** to demultiplexing barcoded samples.
+If a 1D^2 library has been sequenced (requires the FLO-MIN107 flow cell and the SQK-LSK308 script) has been we should invoke the "full_1dsq_basecaller.py" script to get higher identity "squared reads". To perform squared read-pairing, albacore first performs a regular basecalling and then tries to match matching palindromic reads and infer their consensus. This is at the time of writing (Albacore 2.1.3) a computationally expensive process (6x more intensive than a regular Albacore basecalling). If 1D^2 reads are not desired is also possible to basecall the reads using the standard "read_fast5_basecaller.py" with the kit --SQK-LSK108 flag.
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -cwd
+#$ -pe threaded 20
+source /scratch2/software/Python-3.6.0/set-path
+full_1dsq_basecaller.py full_1dsq_basecaller.py --input /scratch2/jon/MinION/BMAN/data_2/reads --worker_threads 20 --save_path /scratch2/jon/MinION/BMAN/albacore_basecall_2 --flowcell FLO-MIN107 --kit SQK-LSK308 --recursive --files_per_batch_folder 0 --output_format fastq --reads_per_fastq_batch 9999999999999
+</code>
 After basecalling is done, merge the "pass" fastq files together. This will be the input for the next step.