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===== Program for analysing NGS data.

http://www.popgen.dk/angsd

Installation:

  1. Using a local folder containing htslib
#download htslib
git clone --recurse-submodules https://github.com/samtools/htslib.git;
#download angsd
git clone https://github.com/angsd/angsd.git;

#install htslib
cd htslib
make

#install angsd
cd ../angsd
make HTSSRC=../htslib
  1. Systemwide installation of htslib
git clone https://github.com/angsd/angsd.git;
cd angsd; make HTSSRC=systemwide
  1. Using htslib submodule
git clone https://github.com/angsd/angsd.git;
cd angsd; make

Notes

  • I've switched over to using htslib for parsing single reads (to allow for CRAM reading, while avoid having to write my own CRAM parser). I'm still using my own readpools. Users should therefore also download and install htslib.
  • If you are on a mac computer and the compilation process complains about a missnig crybtolib library then do 'make CRYPTOLIB=""'

Program has a paper

http://www.biomedcentral.com/1471-2105/15/356/abstract

angsd's Projects

a2a icon a2a

anything to anything

adv_binf_2023_week1 icon adv_binf_2023_week1

Teaching material used in the "Advanced Bioinformatics for Next-Generation Sequencing" class, University of Copenhagen, 2023

angsd icon angsd

Program for analysing NGS data.

bam2prof icon bam2prof

the subprogram in schmutzi but rewritten using htslib

chisquare icon chisquare

small program for sampling from chi-square distribution

grepper icon grepper

Small program for 'grep'ping multiple keys while only iterating over the datafile once.

maf2fasta icon maf2fasta

Program to generate fasta from maf files (multiple alignment files)

misc icon misc

Small usefull program (not finished and not user friendly for other than me)

newick icon newick

Small code for parsing annoying newick trees recursively

reffinder icon reffinder

Program/lib to extract bases from positions in fastafiles

smallbam icon smallbam

33 small BAMs from CEU population, used for testing correctness of angsd

splitbam icon splitbam

Program to split a bam such that a read does not span multiple reads. Assumes

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