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Scripts related to building major-allele references for Bowtie and Bowtie 2

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This collection of scripts are used to build 1KGenomes project-informed major-allele reference genomes for Bowtie 1 and Bowtie 2. The current scripts build linear references with major alleles. We provide SNP-only and SNP-and-indel indexes for both Bowtie versions. The inclusion of indels change the genomic coordinate system. We recommend using levioSAM to perform accurate and scalable lift-over for alignments against the SNP-and-indel indexes.

Downloads

SNP-only

Pre-built major-allele-SNP reference indexes are available:

Aligner Reference Index zip
Bowtie and Bowtie 2 GRCh38 + major SNPs https
Bowtie and Bowtie 2 hg19 + major SNPs https

SNP-and-indel

Pre-built major-allele SNP-and-indel reference indexes are available below. The pre-built levioSAM index (.lft) is also included. We provide a quick example and a detailed tutorial of using levioSAM in a major-allele alignment workflow.

Aligner Reference Index zip
Bowtie and Bowtie 2 GRCh38 + major SNP-and-indels https
Bowtie and Bowtie 2 hg19 + major SNP-and-indels https

Those links will also appear on the Bowtie web page and Bowtie 2 web page in the right-hand sidebar.

The FASTA files with major-allele SNPs inserted are also available:

Reference FASTA file LevioSAM index
GRCh38 + major SNPs https N/A
GRCh38 + major SNP-and-indels https https
hg19 + major SNPs https N/A
hg19 + major SNP-and-indels https https

Instructions

Workflow:

  1. cd to appropriate subdir
  2. ./buildXX.sh to build index
    • Use sbatch buildXX_marcc.sh if on JHU MARCC cluster
  3. ./testXX.sh to test
    • You may see a limited number of warnings, usually due to VCF formatting issues
    • Use sbatch testXX_marcc.sh if on JHU MARCC cluster
  4. ./index_bt_marcc.sh and ./index_bt2_marcc.sh to build Bowtie and Bowtie 2 indexes
    • Use sbatch if on JHU MARCC cluster
  5. ./zip_bt.sh and ./zip_bt2.sh to zip indexes
    • Archives all include README.md
  6. ./scp_bt.sh and ./scp_bt2.sh to copy over to FTP server
    • Assumes you're on MARCC or other JHU cluster with access to gwln1

Requirements for building major-allele FASTAs (first 3 steps above):

Requirements for building genome indexes (4th step above):

Requirement for building major-allele FASTAs including indels (2th step above):

Authors

  • Nae-Chyun Chen
  • Ben Langmead

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