bwa example

exercises/bwa/bwa_batch.sh

+#!/bin/bash
+#SBATCH --mem 150
+#SBATCH --nodes 8
+
+## create an index
+bwa index reference.fa
+
+## perform alignment
+bwa aln -I reference.fa reads.txt > out.sai
+
+## create SAM file
+bwa samse reference.fa out.sai reads.txt > out.sam

exercises/bwa/reference.fa

+>example_reference_1
+GCTGCCCCTGCTTTCCCAGAACCCGGAAGCTCTTCCCCACTTTTCCCAACCCCATGTCCCTGCCTCCCCT
+CAGTTGTGGAGTTACAAGGACAGGCTGTGCTCATGCCAGGTTTGAACTGTGCTCTGGTCTCTCCCCAGTG
+GCCCCTGTGGGTTACGGTTCAGGCAAAACCCACAGGGTGGTGTCCGCATCGTCGGCGGGAAGGCTGCACA
+GCATGGGGCCTGGCCCTGGATGGTCAGCCTCCAGATCTTCACGTACAACAGCCACAGGTACCACACATGT
+GGAGGCAGCTTGCTGAATTCACGATGGGTGCTCACTGCTGCTCACTGCTTCGTCGGCAAAAAGTACGTGT
+AGGGATGCACTGAGGGAGGTCTTCAGAACGGCTCTTCTCAGAGAGGGGCGTTCCCCGGGGATGCTGTGCA
+GCGTCTCCCTGGGGCTCTGGGCCAAGTGGCTGCAAGACTCCGGGGGCTGGTCCAGACCTTTGCTAGGGGA
+AGGCCCTGAGGGTCGCTGTCACCAGGCTTTTGTCCAGCCGGTTGTGACCTGGCTTACCTTTGTGCCCACA
+GTAATGTGCATGACTGGAGACTGGTTTTCGGAGCAAAGGAAATTACATATGGGAACAATAAACCAGTAAA
+GGCGCCTCTGCAAGAGAGATATGTGGAGAAAATCATCATTCATGAAAAATACAACTCTGCGACAGAGGGA
+AATGACATTGCCCTCGTGGAGATCACCCCTCCCATTTCGTGTGGGCGCTTCATTGGGCCGGGCTGCCTGC
+CCCACTTTAAGGCAGGCCTCCCCAGAGGCTCCCAGAGCTGCTGGGTGGCCGGCTGGGGATATATAGAAGA
+GAAAGGTGAGTATGGGAGCGCCTCCAAGGGGGGACGCTGCTGGCCATTCTCCTGGTGGTCTTTGAGGTGC
+AGCGGTCACTTGTTGACACCCAGCCAGGCTGCTTTCATCCTCCTCACGGCGCTACACGTAGAGCCATCAC
+TGTGGCCTTCCACAGTCCCCTGTGCCAGGTCACGTGATGGGTGACTCGTCTGGCTGTCTACGGGGGGGCT
+GACAGCAGGTGCAGGCAGAGCGCAGCGTTGCTTAGAATGGGGTTGAGGCTGTGTCTGTATTTGGCACCTG
+GGGCCCAAGCTGCTGGATCCTGGAAACAAGCAGCAACCCTGAAACAGCCTTTGGAGAAGAGCTCCAGATA
+AGGTTATGTGGCCGTATGACAGTGCCTTCCACTCTCTGGGCCTTGGTTTCCTCATCTGTAAATGGAGGGG
+CTGGATCAGATGGTCTCCAAGCTGACCATTTCCTAACACCTGTGATTCCAGGGCCCAGCCTTCCTGCTTC
+CAGGCTGTCTTTGTCACCATCAGCAGCCACCTCCGGTGCAGTCATAGCACCAAATCTACCCTCTCCATCT
+GAGTTACTTGACATTTGCTCTGTAGACTGGGAAGGGGACCGGTGGTTGGTGTGGCTTTCTGTGGGTCATA
+GGCATCCCTGTATTTCAGGCTTCCTGGAGTGTCCGGCAGGTACCTCTCCATTCAAGACGGGTGTAGCTGT
+CGCTCTAGAGCTCTGTCCATAACCAAGCTGTCTCTCTCTCCCCTGGCTCCCAGAAGATCTCTTGCCCATC
+CAACACTACCTGATACACTCGACACCAGATGAGTTCTAGAAGAGTAGGGGGAATTTCTTCCGTACCAGAC
+CAGGCTCACGGAGGGCCCCAGGTGTGACCTAGAACAAATTGTCATTACTGACTCCGTGGTCAGAGACGCC
+CAGACACCTCTCCCTACATACTTAGGCACACTAGAGATACCATTTATCCCAGAAGCAACAGGTGACCCCA
+TTAAATGGCAGCAGTGAGCAGCAAGGTTTTGCCAGCAGGACAAGACCCAGTAGGACTTGATCTCTGCATG
+TGACCTATACTTCCAGCTTTCCATAAGTGGTGCATCTCAATCTCTTTTTTTCTTGATAATGGATAATGAG
+GCTTCTTAATTCAAGGCAATTCAGTCATATGAGTCTAAAACGCAGCCTTTTTTGGGTAACAACAACAAAA
+AGTCAATAATTTGAGGATTCTTCCTTTAACTCTTATTTCCTTCTCTGAGGGCGTGGTCTAAGTTTCTGAC
+AGGTTTGTCACCTCTCCTGTCCCTCAGGGAAGGGAGTCTCATCCCAGCTGTCCTTGTTCTCACTGGCCTC
+ACTTGACACGTGGCCATCCCCTTCTGGCCTGGAGTGACAGCCTCTATTCCAGCTGCCGATACCCATGGCT
+CTGCCCTGGCCTCTGTCCAGCCCCCTAGCCTGCCATGCTCTGTCCCCTGTCTGATGATGTCCACAGCTCT
+TGGGGGTCCCTATGTTCCTGGGAGGCTGATCTTAGGGTCCCCACTGCCAACCGTTGCTGTCCTATTCTAT
+TACTCAGACAGATTGTAGTGTCCTAGCTATATCTTGGATGCCATGCAAAACCTTTTTTGTTCTGGAATTC
+CCATAAACCTAATAGGATCACTCTGTTTCTGTTTGGGGTTTTTTTGTTTTTCATTTTTGCAAACACATCC
+TGTACCCATAAGCCCAAGTCTTAAAGAAACCCCCAGGCTCCAACTCCTGTGATCCCTTCAAACCTTCCAT
+GTCTTACCACCTCCTTCAACTCATCTGCTTTGGGGCTGGAAGGGTATTGCTTGGGTATTGCTTCTTTCCC
+ATTGGGTTTTGAGTCCCTGCAGACTTTTAAGCATTTGTTATTTAAAGCCCAGGTGTCGGCTGGGTGCAGT
+TGCTCATTCCTGTAATTTACCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGAGTTT
+GAGACCAGCCTGGCCAACATGGTGAAACCCAATCTCTACTAAAAATATAAAACATTAGCAGGGTGTGGTG
+GTGGATGCCTGTTGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGTGAAGG
+TTGCAGTGAGCCAAGATCACGCCACTGCACTCCAGCCTGGGTAACAAGAGCGAAACTTCATCTCAAAAAA
+AACCCGCCAAGGTGTTGGGATTTAGAAAACCCTTTTCTGTTTGAGGACACCTGGCTCTTCACAATAAAAC
+CCATGGCTTTCAAGACTATGGGCTCTGCCCTAGACTTAAAAAGTCATCTTGGCCGGGCGCGGTGGCTCAC
+TCCTGTAATCCCAGCACTTTGGGAGGCCAAGGAGGGTGGATCACAAGGTCGTGAGATCGAGACCATCCTG
+GCTAACACGGTGAAACCTCATTTCTACTAAAAATACAGAAAATTAGCCGGGCATGGTGGCGGGCGCCTGT
+AGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGGCGGAGCTTGCAGTGAGCC
+GAGATGGCGCCACCGCACTCCAGCCTGGGCGACAGAGCAAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA
+ATCGTCTTAATGGCTAATAAGCCAGGATTGTTGTCATTGTTGTTTCAATGTCACCCCTACCCCAAGGGCA
+GTGCATGTACAAAACTCTCACTGCTGCTTGGATGGTAAGAAAAGGTGGGGGCTAAGGGGATTAAAAAACG