From second generation sequencing reads to variant calling. Also variant calling using pairwise whole genome alignment.
To map reads to a target genome and call variants type make map or make breseq.
To get base-by-base reads coverage information type make coverage.
To run a whole genome alignment (with a mask on regions with low coverage),
type make align; this assumes that reads from which de novo assembly has been
derived are present. If they are not present, but a mask is known, just add a
mask.bed file to the top-level directory. If neither masks or reads are
available, the whole genome alignment can be run using the make alignnoreads.
- Reference genome in Fasta and GenBank format
- Map and aligning using reads:
- fastqc
- seq_crumbs
- python and biopython
- seqtk
- bwa
- samtools
- picard
- gatk
- freebayes
- vcflib
- breseq
- Whole genome alignment:
- mummer
- bedtools
- parsnp
Thanks to Omar Wagih (@omarwagih) for some hints on the map pipeline.
Copyright (C) <2015> EMBL-European Bioinformatics Institute
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