Flye
is a de novo assembler for single molecule sequencing reads
(
https://github.com/fenderglass/Flye
)
SMARTdenovo
is an u
ltra-fast de novo assembler using long noisy reads
(
https://github.com/ruanjue/smartdenovo
)
bwa
- Burrows-Wheeler Alignment Tool for mapping low-divergent sequences against a large reference genome
(
http://bio-bwa.sourceforge.net/
)
FREEC
is a tool for the detection of copy-number changes and allelic imbalances using deep-sequencing data
(
https://docs.hpc.qmul.ac.uk/apps/bio/freec/
)
MergeMap
constructs accurate consensus genetic maps from a set of individual genetic maps using DAGs
(
http://www.oligospawn.org/mgmap/
)
Canu
is a hierarchical assembly pipeline for high-noise single-molecule sequencing
(
https://github.com/marbl/canu
)
Racon
is a genomic consensus module to correct raw contigs generated by rapid assembly methods
(
https://github.com/lbcb-sci/racon
)
Unicycler
is an assembly pipeline for bacterial genomes
(
https://github.com/rrwick/Unicycler
)
PanGenie
- Genotyping based on k-mers and pangenome graphs
(
https://bitbucket.org/jana_ebler/pangenie/src/master/
)
Jellyfish
is a tool for fast, memory-efficient counting of k-mers in DNA
(
https://github.com/gmarcais/Jellyfish
)
Long Ranger
is a set of analysis pipelines that processes Chromium sequencing output to align reads
(
https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger
)
Salmon
is a tool for quantifying the expression of transcripts using RNA-seq data
(
https://combine-lab.github.io/salmon/
)
HOME
(histogram of methylation) is a python package for differential methylation region (DMR) identification
(
https://github.com/ListerLab/HOME
)
MUMmer
is a versatile alignment tool for DNA and protein sequences
(
https://github.com/mummer4/mummer
)
AlphaFold
is a package for highly accurate protein structure predictions
(
https://github.com/deepmind/alphafold
)