human mitochondrial genome

mitnanex_human.sh

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+#!/bin/bash
+
+#DEFAULT
+wd="."
+output_folder="mitnanex_results"
+threads=4
+min_qual=0
+
+
+## Help message
+mitnanex_help() {
+    echo "
+    MITNANEX - MITochondrial NANopore reads EXtractor
+
+    Author:
+    Juan Picon Cossio
+
+    Version: 0.1
+
+    Usage: mitnanex.sh [options] FASTQ
+
+    Options:
+        -i        Input file. [required].
+        -t        Threads. [4].
+        -m        Min-len. Filter reads by minimun length. Read seqkit seq documentation. [-1].
+        -M        Max-len. Filter reads by maximun length. Read seqkit seq documentation. [-1].
+        -w        Working directory. Path to create the folder which will contain all mitnanex information. [$wd].
+        -s        Mapping identity. Minimun identity between two reads to be store in the same cluster.[0.6].
+        -q        Min mapping quality (>=). This is for samtools. [0].
+        -f        Flye mode. [--nano-hq]
+        -k        Percentage of reads to keep during filter with filtlong. [80]. 
+        *         Help.
+    "
+    exit 1
+}
+
+
+map_reads(){
+    # Input
+    ## $1=reference
+    ## $2=query
+    ## $3=output
+
+    minimap2 -ax map-ont --split-prefix "temp_prefix" --secondary=no  $1 $2 | samtools view -b --min-MQ $min_qual -F4 -T $1 -o $3
+
+}