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Update docs for v0.1.0 #8

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May 12, 2022
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Update docs for v0.1.0 #8

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6 changes: 6 additions & 0 deletions docs/changelog.md
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Expand Up @@ -6,6 +6,12 @@ nav_order: 99

# Version changelog

**0.1.0**
* Update to CLI
* Add skera `split` / `undo` tools
* Introduce SEGMENT read type
* Bug fixes

**0.0.102**
* Improve runtime

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13 changes: 8 additions & 5 deletions docs/index.md
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Expand Up @@ -22,8 +22,7 @@ _Skera_ splits arrayed PacBio reads at adapter positions generating
([read-segments](/read-segments)). For each input/parent read (e.g. HiFi)
_skera_ will create multiple bam records, one for each fragment. A parent read
can contain many fragments. _Skera_ has two major functions, split and undo.
_Skera_ undo reconstitutes the original parent read from input fragments;
_Skera_ undo is not yet implemented.
_Skera_ undo reconstitutes the original parent read from input fragments.

## Availability
The latest `skera` can be installed via the bioconda.
Expand All @@ -33,7 +32,7 @@ page](https://github.com/PacificBiosciences/pbbioconda) for information on
Installation, Support, License, Copyright, and Disclaimer.

## Versions
Version **0.0.102**: [Full changelog here](/changelog)
Version **0.1.0**: [Full changelog here](/changelog)

## Input
### Reads
Expand All @@ -43,6 +42,10 @@ HiFi reads in PacBio BAM format.
[Adapters](/adapters) in FASTA format.

## Execution
Skera run on HiFi reads in PacBio BAM format:
Skera split run on HiFi reads in PacBio BAM format:

skera <movie>.hifi_reads.bam adapters.fasta <movie>.skera.bam
skera split <movie>.hifi_reads.bam adapters.fasta <movie>.skera.bam

Skera undo:

skera undo <movie>.skera.bam <movie>.undo.bam