diff --git a/README.md b/README.md
index 47f3b05f58421ee5393c80c35303de10aeed22ed..255bdd69fce59c271800da3ff3c0328a04830127 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,13 @@
A modularized version of the program [PopIns2](https://github.com/kehrlab/PopIns2) for population-scale detection of non-reference sequence variants.
-__Note: The recommended way to run popins4snake is via the Snakemake workflow [*PopinSnake*](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake).__
+
+*Popins4snake* is a program consisting of several functions.
+The functions are designed to be chained into a workflow, together with calls to standard bioinformatics programs (samtools, bwa, ...) and bash commands.
+
+__The recommended way of running *popins4snake* is using the Snakemake workflow [PopinSnake](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake).__
+
+You can find installation instructions for all dependencies of the PopinSnake workflow, including instructions for installing popins4snake in the [PopinSnake README file](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake/-/blob/main/README.md).
@@ -11,6 +17,7 @@ __Note: The recommended way to run popins4snake is via the Snakemake workflow [*
1. [Requirements](#requirements)
1. [Installation](#installation)
1. [Usage](#usage)
+1. [Summary of popins4snake functions](#summary-of-popins4snake-functions)
1. [Help](#help)
1. [References](#references)
@@ -82,95 +89,92 @@ The [PopIns2 Wiki](https://github.com/kehrlab/PopIns2/wiki/Troubleshooting---FAQ
## Usage
-*Popins4snake* is a program consisting of several functions.
-The functions are designed to be chained into a workflow together with calls to standard bioinformatics programs (samtools, bwa, ...) and bash commands.
-__The recommended way of running *popins4snake* is using the Snakemake workflow [PopinSnake](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake).__
-To display the help page of each of the *popins4snake* function, type `popins2 <command> --help` as shown in the [help section](#help).
+To get an overview of the functions offered in *popins4snake*, you can run `./popins4snake -h` after installation:
+```
+=====================================================================
+A modularized version of the program PopIns2
+ for population-scale detection of non-reference sequence variants
+=====================================================================
+
+SYNOPSIS
+ ./popins4snake COMMAND [OPTIONS]
-### The `crop-unmapped` command
+COMMAND
+ crop-unmapped Extract unmapped and poorly aligned reads from a BAM file.
+ merge-bams Merge two name-sorted BAM files of the same sample and set mate information of now paired reads.
+ merge-contigs Merge sets of contigs into supercontigs using a colored compacted de Bruijn Graph.
+ find-locations Find insertion locations of (super-)contigs per sample.
+ merge-locations Merge insertion locations from all samples into one file.
+ place-refalign Find positions of (super-)contigs by aligning contig ends to the reference genome.
+ place-splitalign Find positions of (super-)contigs by split-read alignment (per sample).
+ place-finish Combine (super-)contig positions found by split-read alignment from all samples.
+ genotype Determine genotypes of all insertions in a sample.
+
+VERSION
+ 0.1.0-a52d4f5, Date: 2022-08-25 14:42:31
+
+Try `../popins4snake/popins4snake COMMAND --help' for more information on each command.
```
-popins2 crop-unmapped [OPTIONS] sample.bam
+
+
+
+## Summary of *popins4snake* functions
+
+To display the help page of each of the *popins4snake* functions, type `./popins4snake <command> --help`.
+
+
+### The `crop-unmapped` function
+```
+popins4snake crop-unmapped [OPTIONS] sample.bam
```
The crop-unmapped command identifies reads without high-quality alignment to the reference genome. The reads given in the input BAM file must be indexed, i.e. the file `sample.bam.bai` is expected to exist.
-### The `merge-bams` command
+### The `merge-bams` function
```
-popins2 merge-bams [OPTIONS] input1.bam input2.bam
+popins4snake merge-bams [OPTIONS] input1.bam input2.bam
```
-### The `merge-contigs` command
+### The `merge-contigs` function
```
-popins2 merge-contigs [OPTIONS] {-s|-r} /path/to/sample_directories/
+popins4snake merge-contigs [OPTIONS] {-s|-r} /path/to/sample_directories/
```
\[Default\] The merge command builds a colored and compacted de Bruijn Graph (ccdbg) of all contigs of all samples in a given source directory _DIR_.
By default, the merge module finds all files of the pattern `<DIR>/*/assembly_final.contigs.fa`. To process the contigs of the [assemble command](#the-assemble-command) the __-r__ input parameter is recommended. Once the ccdbg is built, the merge module identifies paths in the graph and returns _supercontigs_.
```
-popins2 merge [OPTIONS] -y input.gfa -z input.bfg_colors
+popins4snake merge-contigs [OPTIONS] -y input.gfa -z input.bfg_colors
```
An alternative way of providing input for the merge command is to directly pass a ccdbg. Here, the merge command expects a _GFA_ file and a _bfg_colors_ file, which is specific to the Bifrost. If you choose to run the merge command with a _pre_-built GFA graph, mind that you have to set the Algorithm options accordingly (in particular __-k__).
-### The `find-locations` command
+### The `find-locations` function
```
-popins2 find-locations [OPTIONS] SAMPLE_ID
+popins4snake find-locations [OPTIONS] SAMPLE_ID
```
-### The `merge-locations` command
+### The `merge-locations` function
```
-popins2 merge-locations [OPTIONS]
+popins4snake merge-locations [OPTIONS]
```
-### The `place` commands
+### The `place` function
```
-popins2 place-refalign [OPTIONS]
-popins2 place-splitalign [OPTIONS] SAMPLE_ID
-popins2 place-finish [OPTIONS]
+popins4snake place-refalign [OPTIONS]
+popins4snake place-splitalign [OPTIONS] SAMPLE_ID
+popins4snake place-finish [OPTIONS]
```
In brief, the place commands attempt to anker the supercontigs to the samples. At first, all potential anker locations from all samples are collected. Then prefixes/suffixes of the supercontigs are aligned to all collected locations. For successful alignments records are written to a VCF file. In the second step, all remaining locations are split-aligned per sample. Finally, all locations from all successful split-alignments are combined and added to the VCF file.
-### The `genotype` command
+### The `genotype` function
```
-popins2 genotype [OPTIONS] SAMPLE_ID
+popins4snake genotype [OPTIONS] SAMPLE_ID
```
The genotype command generates alleles (ALT) of the supercontigs with some flanking reference genome sequence. Then, the reads of a sample are aligned to ALT and the reference genome around the breakpoint (REF). The ratio of alignments to ALT and REF determines a genotype quality and a final genotype prediction per variant per sample.
-
-
-
-## Help
-
-```
-$ popins4snake -h
-
-=====================================================================
-A modularized version of the program PopIns2
- for population-scale detection of non-reference sequence variants
-=====================================================================
-
-SYNOPSIS
- ../popins4snake/popins4snake COMMAND [OPTIONS]
-
-COMMAND
- crop-unmapped Extract unmapped and poorly aligned reads from a BAM file.
- merge-bams Merge two name-sorted BAM files of the same sample and set mate information of now paired reads.
- merge-contigs Merge sets of contigs into supercontigs using a colored compacted de Bruijn Graph.
- find-locations Find insertion locations of (super-)contigs per sample.
- merge-locations Merge insertion locations from all samples into one file.
- place-refalign Find positions of (super-)contigs by aligning contig ends to the reference genome.
- place-splitalign Find positions of (super-)contigs by split-read alignment (per sample).
- place-finish Combine (super-)contig positions found by split-read alignment from all samples.
- genotype Determine genotypes of all insertions in a sample.
-
-VERSION
- 0.1.0-a52d4f5, Date: 2022-08-25 14:42:31
-
-Try `../popins4snake/popins4snake COMMAND --help' for more information on each command.
-```