README.md
setup.py
iva/__init__.py
iva/assembly.py
iva/common.py
iva/contig.py
iva/contig_trim.py
iva/edge.py
iva/egg_extract.py
iva/external_progs.py
iva/graph.py
iva/kcount.py
iva/kmers.py
iva/kraken.py
iva/mapping.py
iva/mummer.py
iva/qc.py
iva/qc_external.py
iva/read_trim.py
iva/seed.py
iva/seed_processor.py
iva/test_data_runner.py
iva.egg-info/PKG-INFO
iva.egg-info/SOURCES.txt
iva.egg-info/dependency_links.txt
iva.egg-info/requires.txt
iva.egg-info/top_level.txt
iva/gage/GetFastaStats$ContigAt.class
iva/gage/GetFastaStats.class
iva/gage/GetFastaStats.java
iva/gage/SizeFasta.class
iva/gage/SizeFasta.java
iva/gage/SplitFastaByLetter.class
iva/gage/SplitFastaByLetter.java
iva/gage/Utils$Pair.class
iva/gage/Utils$ToProtein.class
iva/gage/Utils$Translate.class
iva/gage/Utils.class
iva/gage/Utils.java
iva/gage/colsum.pl
iva/gage/getCorrectnessStats.sh
iva/gage/getMummerStats.sh
iva/gage/getScaffoldStats$1.class
iva/gage/getScaffoldStats$Scaffold.class
iva/gage/getScaffoldStats.class
iva/gage/getScaffoldStats.java
iva/ratt/embl2gff.pl
iva/ratt/genbank2embl.pl
iva/ratt/main.ratt.pl
iva/ratt/ratt.config
iva/ratt/ratt.config.hiv
iva/ratt/ratt_correction.pm
iva/ratt/start.ratt.sh
iva/read_trim/adapters.fasta
iva/test_run_data/hiv_pcr_primers.fa
iva/test_run_data/iva_contigs_no_trimmomatic.fasta
iva/test_run_data/iva_contigs_with_trimmomatic.fasta
iva/test_run_data/reads_1.fq.gz
iva/test_run_data/reads_2.fq.gz
iva/test_run_data/reference.fasta
scripts/iva
scripts/iva_qc
scripts/iva_qc_make_db